HEADER TRANSFERASE 11-AUG-09 3IN1 TITLE CRYSTAL STRUCTURE OF A PUTATIVE RIBOKINASE IN COMPLEX WITH ADP FROM TITLE 2 E.COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED SUGAR KINASE YDJH; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: STRAIN K12; SOURCE 5 GENE: B1772, JW5289, YDJH, YDJH/B1772/JW5289; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODON+RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: BC PSGX3 (BC); SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PSGX3 KEYWDS RIBOKINASE, TRANSFERASE, PFKB FAMILY, SUGAR KINASE YDJH, ADP NYSGXRC, KEYWDS 2 11206A, PSI2, KINASE, STRUCTURAL GENOMICS, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR L.SATYANARAYANA,S.K.BURLEY,S.SWAMINATHAN,NEW YORK SGX RESEARCH CENTER AUTHOR 2 FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 5 27-NOV-24 3IN1 1 REMARK REVDAT 4 22-NOV-23 3IN1 1 REMARK REVDAT 3 06-SEP-23 3IN1 1 REMARK REVDAT 2 10-FEB-21 3IN1 1 AUTHOR JRNL REMARK SEQADV REVDAT 2 2 1 LINK REVDAT 1 08-SEP-09 3IN1 0 JRNL AUTH L.SATYANARAYANA,S.K.BURLEY,S.SWAMINATHAN JRNL TITL CRYSTAL STRUCTURE OF A PUTATIVE RIBOKINASE IN COMPLEX WITH JRNL TITL 2 ADP FROM E.COLI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 40897 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1642 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 272 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4736 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 195 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.15000 REMARK 3 B22 (A**2) : -1.36600 REMARK 3 B33 (A**2) : -3.78400 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.23 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.475 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.349 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.676 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.931 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : ADP.PAR.TXT REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3IN1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054615. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43219 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.61500 REMARK 200 FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MOLECULAR REPLACEMENT REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLREP REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3H49 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM ACETATE, 30% PEG 4K, REMARK 280 SODIUM CITRATE 5.6PH, 10% ISOPROPANOL, 10MM ADP SODIUM SALT, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K, PH 5.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 37.78850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.30400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.15050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.30400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.78850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.15050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 151.15400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 44.15050 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 58.30400 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 151.15400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -44.15050 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 58.30400 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MSE A -1 REMARK 465 SER A 0 REMARK 465 LEU A 1 REMARK 465 ASP A 2 REMARK 465 GLY A 315 REMARK 465 GLU A 316 REMARK 465 GLY A 317 REMARK 465 HIS A 318 REMARK 465 HIS A 319 REMARK 465 HIS A 320 REMARK 465 HIS A 321 REMARK 465 HIS A 322 REMARK 465 HIS A 323 REMARK 465 MSE B -1 REMARK 465 SER B 0 REMARK 465 LEU B 1 REMARK 465 ASP B 2 REMARK 465 GLY B 315 REMARK 465 GLU B 316 REMARK 465 GLY B 317 REMARK 465 HIS B 318 REMARK 465 HIS B 319 REMARK 465 HIS B 320 REMARK 465 HIS B 321 REMARK 465 HIS B 322 REMARK 465 HIS B 323 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ALA A 162 N - CA - C ANGL. DEV. = -23.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 24 67.95 -107.75 REMARK 500 GLU A 104 45.21 -69.13 REMARK 500 ASP A 105 -18.80 -157.20 REMARK 500 ALA A 140 79.01 -66.70 REMARK 500 SER A 141 100.28 87.93 REMARK 500 PHE A 143 -17.35 84.91 REMARK 500 ARG A 163 -5.44 91.49 REMARK 500 PHE A 194 70.19 -116.45 REMARK 500 ASN A 302 -117.07 -135.47 REMARK 500 ARG A 303 -38.92 -142.70 REMARK 500 ASP B 27 106.06 71.79 REMARK 500 VAL B 28 -69.64 146.43 REMARK 500 ASP B 29 -25.99 101.93 REMARK 500 SER B 141 94.27 89.21 REMARK 500 PHE B 143 -18.13 85.67 REMARK 500 PHE B 194 70.20 -119.39 REMARK 500 ASP B 239 -39.29 76.92 REMARK 500 ALA B 252 92.80 100.40 REMARK 500 GLU B 312 22.96 97.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 411 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 259 N REMARK 620 2 ADP A 510 O2A 108.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 411 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3H49 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A PUTATIVE RIBOKINASE (APO FORM) FROM E.COLI REMARK 900 AT 1.8A RESOLUTION REMARK 900 RELATED ID: 3I3Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RIBOKINASE IN COMPLEX WITH D-RIBOSE FROM REMARK 900 KLEBSIELLA PNEUMONIAE REMARK 900 RELATED ID: 3IKH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RIBOKINASE IN COMPLEX WITH ATP AND GLYCEROL IN REMARK 900 THE ACTIVE SITE FROM KLEBSIELLA PNEUMONIAE REMARK 900 RELATED ID: 3HIC RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF PHOSPHOFRUCTOKINASE(LIN2199)FROM LISTERIA REMARK 900 INNOCUA REMARK 900 RELATED ID: 3IE7 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF PHOSPHOFRUCTOKINASE (LIN2199) FROM REMARK 900 LISTERIA INNOCUA IN COMPLEX WITH ATP AT 1.6A REMARK 900 RELATED ID: NYSGXRC-11206A RELATED DB: TARGETDB DBREF 3IN1 A 2 315 UNP P77493 YDJH_ECOLI 2 315 DBREF 3IN1 B 2 315 UNP P77493 YDJH_ECOLI 2 315 SEQADV 3IN1 MSE A -1 UNP P77493 EXPRESSION TAG SEQADV 3IN1 SER A 0 UNP P77493 EXPRESSION TAG SEQADV 3IN1 LEU A 1 UNP P77493 EXPRESSION TAG SEQADV 3IN1 GLU A 316 UNP P77493 EXPRESSION TAG SEQADV 3IN1 GLY A 317 UNP P77493 EXPRESSION TAG SEQADV 3IN1 HIS A 318 UNP P77493 EXPRESSION TAG SEQADV 3IN1 HIS A 319 UNP P77493 EXPRESSION TAG SEQADV 3IN1 HIS A 320 UNP P77493 EXPRESSION TAG SEQADV 3IN1 HIS A 321 UNP P77493 EXPRESSION TAG SEQADV 3IN1 HIS A 322 UNP P77493 EXPRESSION TAG SEQADV 3IN1 HIS A 323 UNP P77493 EXPRESSION TAG SEQADV 3IN1 MSE B -1 UNP P77493 EXPRESSION TAG SEQADV 3IN1 SER B 0 UNP P77493 EXPRESSION TAG SEQADV 3IN1 LEU B 1 UNP P77493 EXPRESSION TAG SEQADV 3IN1 GLU B 316 UNP P77493 EXPRESSION TAG SEQADV 3IN1 GLY B 317 UNP P77493 EXPRESSION TAG SEQADV 3IN1 HIS B 318 UNP P77493 EXPRESSION TAG SEQADV 3IN1 HIS B 319 UNP P77493 EXPRESSION TAG SEQADV 3IN1 HIS B 320 UNP P77493 EXPRESSION TAG SEQADV 3IN1 HIS B 321 UNP P77493 EXPRESSION TAG SEQADV 3IN1 HIS B 322 UNP P77493 EXPRESSION TAG SEQADV 3IN1 HIS B 323 UNP P77493 EXPRESSION TAG SEQRES 1 A 325 MSE SER LEU ASP ASN LEU ASP VAL ILE CYS ILE GLY ALA SEQRES 2 A 325 ALA ILE VAL ASP ILE PRO LEU GLN PRO VAL SER LYS ASN SEQRES 3 A 325 ILE PHE ASP VAL ASP SER TYR PRO LEU GLU ARG ILE ALA SEQRES 4 A 325 MSE THR THR GLY GLY ASP ALA ILE ASN GLU ALA THR ILE SEQRES 5 A 325 ILE SER ARG LEU GLY HIS ARG THR ALA LEU MSE SER ARG SEQRES 6 A 325 ILE GLY LYS ASP ALA ALA GLY GLN PHE ILE LEU ASP HIS SEQRES 7 A 325 CYS ARG LYS GLU ASN ILE ASP ILE GLN SER LEU LYS GLN SEQRES 8 A 325 ASP VAL SER ILE ASP THR SER ILE ASN VAL GLY LEU VAL SEQRES 9 A 325 THR GLU ASP GLY GLU ARG THR PHE VAL THR ASN ARG ASN SEQRES 10 A 325 GLY SER LEU TRP LYS LEU ASN ILE ASP ASP VAL ASP PHE SEQRES 11 A 325 ALA ARG PHE SER GLN ALA LYS LEU LEU SER LEU ALA SER SEQRES 12 A 325 ILE PHE ASN SER PRO LEU LEU ASP GLY LYS ALA LEU THR SEQRES 13 A 325 GLU ILE PHE THR GLN ALA LYS ALA ARG GLN MSE ILE ILE SEQRES 14 A 325 CYS ALA ASP MSE ILE LYS PRO ARG LEU ASN GLU THR LEU SEQRES 15 A 325 ASP ASP ILE CYS GLU ALA LEU SER TYR VAL ASP TYR LEU SEQRES 16 A 325 PHE PRO ASN PHE ALA GLU ALA LYS LEU LEU THR GLY LYS SEQRES 17 A 325 GLU THR LEU ASP GLU ILE ALA ASP CYS PHE LEU ALA CYS SEQRES 18 A 325 GLY VAL LYS THR VAL VAL ILE LYS THR GLY LYS ASP GLY SEQRES 19 A 325 CYS PHE ILE LYS ARG GLY ASP MSE THR MSE LYS VAL PRO SEQRES 20 A 325 ALA VAL ALA GLY ILE THR ALA ILE ASP THR ILE GLY ALA SEQRES 21 A 325 GLY ASP ASN PHE ALA SER GLY PHE ILE ALA ALA LEU LEU SEQRES 22 A 325 GLU GLY LYS ASN LEU ARG GLU CYS ALA ARG PHE ALA ASN SEQRES 23 A 325 ALA THR ALA ALA ILE SER VAL LEU SER VAL GLY ALA THR SEQRES 24 A 325 THR GLY VAL LYS ASN ARG LYS LEU VAL GLU GLN LEU LEU SEQRES 25 A 325 GLU GLU TYR GLU GLY GLU GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 325 MSE SER LEU ASP ASN LEU ASP VAL ILE CYS ILE GLY ALA SEQRES 2 B 325 ALA ILE VAL ASP ILE PRO LEU GLN PRO VAL SER LYS ASN SEQRES 3 B 325 ILE PHE ASP VAL ASP SER TYR PRO LEU GLU ARG ILE ALA SEQRES 4 B 325 MSE THR THR GLY GLY ASP ALA ILE ASN GLU ALA THR ILE SEQRES 5 B 325 ILE SER ARG LEU GLY HIS ARG THR ALA LEU MSE SER ARG SEQRES 6 B 325 ILE GLY LYS ASP ALA ALA GLY GLN PHE ILE LEU ASP HIS SEQRES 7 B 325 CYS ARG LYS GLU ASN ILE ASP ILE GLN SER LEU LYS GLN SEQRES 8 B 325 ASP VAL SER ILE ASP THR SER ILE ASN VAL GLY LEU VAL SEQRES 9 B 325 THR GLU ASP GLY GLU ARG THR PHE VAL THR ASN ARG ASN SEQRES 10 B 325 GLY SER LEU TRP LYS LEU ASN ILE ASP ASP VAL ASP PHE SEQRES 11 B 325 ALA ARG PHE SER GLN ALA LYS LEU LEU SER LEU ALA SER SEQRES 12 B 325 ILE PHE ASN SER PRO LEU LEU ASP GLY LYS ALA LEU THR SEQRES 13 B 325 GLU ILE PHE THR GLN ALA LYS ALA ARG GLN MSE ILE ILE SEQRES 14 B 325 CYS ALA ASP MSE ILE LYS PRO ARG LEU ASN GLU THR LEU SEQRES 15 B 325 ASP ASP ILE CYS GLU ALA LEU SER TYR VAL ASP TYR LEU SEQRES 16 B 325 PHE PRO ASN PHE ALA GLU ALA LYS LEU LEU THR GLY LYS SEQRES 17 B 325 GLU THR LEU ASP GLU ILE ALA ASP CYS PHE LEU ALA CYS SEQRES 18 B 325 GLY VAL LYS THR VAL VAL ILE LYS THR GLY LYS ASP GLY SEQRES 19 B 325 CYS PHE ILE LYS ARG GLY ASP MSE THR MSE LYS VAL PRO SEQRES 20 B 325 ALA VAL ALA GLY ILE THR ALA ILE ASP THR ILE GLY ALA SEQRES 21 B 325 GLY ASP ASN PHE ALA SER GLY PHE ILE ALA ALA LEU LEU SEQRES 22 B 325 GLU GLY LYS ASN LEU ARG GLU CYS ALA ARG PHE ALA ASN SEQRES 23 B 325 ALA THR ALA ALA ILE SER VAL LEU SER VAL GLY ALA THR SEQRES 24 B 325 THR GLY VAL LYS ASN ARG LYS LEU VAL GLU GLN LEU LEU SEQRES 25 B 325 GLU GLU TYR GLU GLY GLU GLY HIS HIS HIS HIS HIS HIS MODRES 3IN1 MSE A 38 MET SELENOMETHIONINE MODRES 3IN1 MSE A 61 MET SELENOMETHIONINE MODRES 3IN1 MSE A 165 MET SELENOMETHIONINE MODRES 3IN1 MSE A 171 MET SELENOMETHIONINE MODRES 3IN1 MSE A 240 MET SELENOMETHIONINE MODRES 3IN1 MSE A 242 MET SELENOMETHIONINE MODRES 3IN1 MSE B 38 MET SELENOMETHIONINE MODRES 3IN1 MSE B 61 MET SELENOMETHIONINE MODRES 3IN1 MSE B 165 MET SELENOMETHIONINE MODRES 3IN1 MSE B 171 MET SELENOMETHIONINE MODRES 3IN1 MSE B 240 MET SELENOMETHIONINE MODRES 3IN1 MSE B 242 MET SELENOMETHIONINE HET MSE A 38 8 HET MSE A 61 8 HET MSE A 165 8 HET MSE A 171 8 HET MSE A 240 8 HET MSE A 242 8 HET MSE B 38 8 HET MSE B 61 8 HET MSE B 165 8 HET MSE B 171 8 HET MSE B 240 8 HET MSE B 242 8 HET ADP A 510 27 HET NA A 411 1 HET ADP B 510 27 HET NA B 411 1 HETNAM MSE SELENOMETHIONINE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM NA SODIUM ION FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 NA 2(NA 1+) FORMUL 7 HOH *195(H2 O) HELIX 1 1 ASN A 24 VAL A 28 5 5 HELIX 2 2 GLY A 42 LEU A 54 1 13 HELIX 3 3 ASP A 67 ASN A 81 1 15 HELIX 4 4 GLY A 116 LEU A 121 1 6 HELIX 5 5 ASN A 122 VAL A 126 5 5 HELIX 6 6 ASP A 127 ALA A 134 5 8 HELIX 7 7 ASP A 149 ALA A 162 1 14 HELIX 8 8 THR A 179 ASP A 182 5 4 HELIX 9 9 ILE A 183 SER A 188 1 6 HELIX 10 10 ASN A 196 GLY A 205 1 10 HELIX 11 11 THR A 208 CYS A 219 1 12 HELIX 12 12 GLY A 229 ASP A 231 5 3 HELIX 13 13 GLY A 257 GLU A 272 1 16 HELIX 14 14 ASN A 275 LEU A 292 1 18 HELIX 15 15 ARG A 303 GLU A 312 1 10 HELIX 16 16 GLY B 42 LEU B 54 1 13 HELIX 17 17 ASP B 67 ASN B 81 1 15 HELIX 18 18 GLY B 116 LEU B 121 1 6 HELIX 19 19 ASN B 122 VAL B 126 5 5 HELIX 20 20 ASP B 127 ALA B 134 5 8 HELIX 21 21 ASP B 149 ALA B 162 1 14 HELIX 22 22 THR B 179 ASP B 182 5 4 HELIX 23 23 ILE B 183 SER B 188 1 6 HELIX 24 24 ASN B 196 GLY B 205 1 10 HELIX 25 25 THR B 208 CYS B 219 1 12 HELIX 26 26 GLY B 229 ASP B 231 5 3 HELIX 27 27 GLY B 257 GLU B 272 1 16 HELIX 28 28 ASN B 275 LEU B 292 1 18 HELIX 29 29 ASN B 302 GLU B 311 1 10 SHEET 1 A 9 LEU A 87 ASP A 90 0 SHEET 2 A 9 THR A 58 GLY A 65 1 N ILE A 64 O LYS A 88 SHEET 3 A 9 VAL A 6 ILE A 9 1 N CYS A 8 O ALA A 59 SHEET 4 A 9 LEU A 136 ILE A 142 1 O SER A 138 N ILE A 7 SHEET 5 A 9 ILE A 166 MSE A 171 1 O ILE A 166 N LEU A 137 SHEET 6 A 9 TYR A 192 PHE A 194 1 O PHE A 194 N ALA A 169 SHEET 7 A 9 THR A 223 LYS A 227 1 O VAL A 225 N LEU A 193 SHEET 8 A 9 CYS A 233 ARG A 237 -1 O PHE A 234 N ILE A 226 SHEET 9 A 9 MSE A 240 VAL A 244 -1 O MSE A 242 N ILE A 235 SHEET 1 B 4 THR A 39 GLY A 41 0 SHEET 2 B 4 ILE A 13 VAL A 21 -1 N ASP A 15 O THR A 39 SHEET 3 B 4 ILE A 97 THR A 103 1 O GLY A 100 N LEU A 18 SHEET 4 B 4 ARG A 108 VAL A 111 -1 O VAL A 111 N VAL A 99 SHEET 1 C 9 LEU B 87 ASP B 90 0 SHEET 2 C 9 ARG B 57 GLY B 65 1 N ILE B 64 O LYS B 88 SHEET 3 C 9 LEU B 4 ILE B 9 1 N CYS B 8 O MSE B 61 SHEET 4 C 9 LEU B 136 ILE B 142 1 O SER B 138 N ILE B 7 SHEET 5 C 9 ILE B 166 MSE B 171 1 O CYS B 168 N LEU B 137 SHEET 6 C 9 TYR B 192 PHE B 194 1 O PHE B 194 N ALA B 169 SHEET 7 C 9 THR B 223 LYS B 227 1 O VAL B 225 N LEU B 193 SHEET 8 C 9 CYS B 233 LYS B 236 -1 O PHE B 234 N ILE B 226 SHEET 9 C 9 THR B 241 VAL B 244 -1 O MSE B 242 N ILE B 235 SHEET 1 D 4 THR B 39 GLY B 41 0 SHEET 2 D 4 ILE B 13 VAL B 21 -1 N ASP B 15 O THR B 39 SHEET 3 D 4 ILE B 97 THR B 103 1 O GLY B 100 N LEU B 18 SHEET 4 D 4 ARG B 108 VAL B 111 -1 O THR B 109 N LEU B 101 SSBOND 1 CYS A 184 CYS A 219 1555 1555 2.06 SSBOND 2 CYS B 184 CYS B 219 1555 1555 2.05 LINK C ALA A 37 N MSE A 38 1555 1555 1.33 LINK C MSE A 38 N THR A 39 1555 1555 1.33 LINK C LEU A 60 N MSE A 61 1555 1555 1.33 LINK C MSE A 61 N SER A 62 1555 1555 1.32 LINK C GLN A 164 N MSE A 165 1555 1555 1.33 LINK C MSE A 165 N ILE A 166 1555 1555 1.33 LINK C ASP A 170 N MSE A 171 1555 1555 1.33 LINK C MSE A 171 N ILE A 172 1555 1555 1.33 LINK C ASP A 239 N MSE A 240 1555 1555 1.33 LINK C MSE A 240 N THR A 241 1555 1555 1.33 LINK C THR A 241 N MSE A 242 1555 1555 1.32 LINK C MSE A 242 N LYS A 243 1555 1555 1.33 LINK C ALA B 37 N MSE B 38 1555 1555 1.33 LINK C MSE B 38 N THR B 39 1555 1555 1.32 LINK C LEU B 60 N MSE B 61 1555 1555 1.33 LINK C MSE B 61 N SER B 62 1555 1555 1.32 LINK C GLN B 164 N MSE B 165 1555 1555 1.32 LINK C MSE B 165 N ILE B 166 1555 1555 1.33 LINK C ASP B 170 N MSE B 171 1555 1555 1.33 LINK C MSE B 171 N ILE B 172 1555 1555 1.33 LINK C ASP B 239 N MSE B 240 1555 1555 1.33 LINK C MSE B 240 N THR B 241 1555 1555 1.33 LINK C THR B 241 N MSE B 242 1555 1555 1.33 LINK C MSE B 242 N LYS B 243 1555 1555 1.33 LINK N GLY A 259 NA NA A 411 1555 1555 2.82 LINK NA NA A 411 O2A ADP A 510 1555 1555 2.73 LINK NA NA B 411 O2A ADP B 510 1555 1555 2.78 CISPEP 1 GLN A 19 PRO A 20 0 -0.29 CISPEP 2 GLN B 19 PRO B 20 0 -0.67 SITE 1 AC1 13 ASN A 196 LYS A 227 GLY A 229 LYS A 230 SITE 2 AC1 13 GLY A 232 ALA A 246 THR A 255 ASN A 284 SITE 3 AC1 13 ALA A 287 HOH A 394 NA A 411 HOH A 414 SITE 4 AC1 13 HOH A 417 SITE 1 AC2 4 THR A 255 ALA A 258 GLY A 259 ADP A 510 SITE 1 AC3 14 ASN B 196 LYS B 227 GLY B 229 GLY B 232 SITE 2 AC3 14 ALA B 246 VAL B 247 ILE B 250 ALA B 252 SITE 3 AC3 14 THR B 255 ASN B 284 ALA B 287 HOH B 385 SITE 4 AC3 14 NA B 411 HOH B 421 SITE 1 AC4 2 GLY B 259 ADP B 510 CRYST1 75.577 88.301 116.608 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013232 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011325 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008576 0.00000 CONECT 265 268 CONECT 268 265 269 CONECT 269 268 270 272 CONECT 270 269 271 276 CONECT 271 270 CONECT 272 269 273 CONECT 273 272 274 CONECT 274 273 275 CONECT 275 274 CONECT 276 270 CONECT 428 434 CONECT 434 428 435 CONECT 435 434 436 438 CONECT 436 435 437 442 CONECT 437 436 CONECT 438 435 439 CONECT 439 438 440 CONECT 440 439 441 CONECT 441 440 CONECT 442 436 CONECT 1240 1247 CONECT 1247 1240 1248 CONECT 1248 1247 1249 1251 CONECT 1249 1248 1250 1255 CONECT 1250 1249 CONECT 1251 1248 1252 CONECT 1252 1251 1253 CONECT 1253 1252 1254 CONECT 1254 1253 CONECT 1255 1249 CONECT 1284 1290 CONECT 1290 1284 1291 CONECT 1291 1290 1292 1294 CONECT 1292 1291 1293 1298 CONECT 1293 1292 CONECT 1294 1291 1295 CONECT 1295 1294 1296 CONECT 1296 1295 1297 CONECT 1297 1296 CONECT 1298 1292 CONECT 1402 1676 CONECT 1676 1402 CONECT 1818 1824 CONECT 1824 1818 1825 CONECT 1825 1824 1826 1828 CONECT 1826 1825 1827 1832 CONECT 1827 1826 CONECT 1828 1825 1829 CONECT 1829 1828 1830 CONECT 1830 1829 1831 CONECT 1831 1830 CONECT 1832 1826 CONECT 1834 1839 CONECT 1839 1834 1840 CONECT 1840 1839 1841 1843 CONECT 1841 1840 1842 1847 CONECT 1842 1841 CONECT 1843 1840 1844 CONECT 1844 1843 1845 CONECT 1845 1844 1846 CONECT 1846 1845 CONECT 1847 1841 CONECT 1951 4766 CONECT 2634 2637 CONECT 2637 2634 2638 CONECT 2638 2637 2639 2641 CONECT 2639 2638 2640 2645 CONECT 2640 2639 CONECT 2641 2638 2642 CONECT 2642 2641 2643 CONECT 2643 2642 2644 CONECT 2644 2643 CONECT 2645 2639 CONECT 2797 2803 CONECT 2803 2797 2804 CONECT 2804 2803 2805 2807 CONECT 2805 2804 2806 2811 CONECT 2806 2805 CONECT 2807 2804 2808 CONECT 2808 2807 2809 CONECT 2809 2808 2810 CONECT 2810 2809 CONECT 2811 2805 CONECT 3609 3616 CONECT 3616 3609 3617 CONECT 3617 3616 3618 3620 CONECT 3618 3617 3619 3624 CONECT 3619 3618 CONECT 3620 3617 3621 CONECT 3621 3620 3622 CONECT 3622 3621 3623 CONECT 3623 3622 CONECT 3624 3618 CONECT 3653 3659 CONECT 3659 3653 3660 CONECT 3660 3659 3661 3663 CONECT 3661 3660 3662 3667 CONECT 3662 3661 CONECT 3663 3660 3664 CONECT 3664 3663 3665 CONECT 3665 3664 3666 CONECT 3666 3665 CONECT 3667 3661 CONECT 3771 4045 CONECT 4045 3771 CONECT 4187 4193 CONECT 4193 4187 4194 CONECT 4194 4193 4195 4197 CONECT 4195 4194 4196 4201 CONECT 4196 4195 CONECT 4197 4194 4198 CONECT 4198 4197 4199 CONECT 4199 4198 4200 CONECT 4200 4199 CONECT 4201 4195 CONECT 4203 4208 CONECT 4208 4203 4209 CONECT 4209 4208 4210 4212 CONECT 4210 4209 4211 4216 CONECT 4211 4210 CONECT 4212 4209 4213 CONECT 4213 4212 4214 CONECT 4214 4213 4215 CONECT 4215 4214 CONECT 4216 4210 CONECT 4739 4740 4741 4742 4746 CONECT 4740 4739 CONECT 4741 4739 CONECT 4742 4739 CONECT 4743 4744 4745 4746 4747 CONECT 4744 4743 CONECT 4745 4743 4766 CONECT 4746 4739 4743 CONECT 4747 4743 4748 CONECT 4748 4747 4749 CONECT 4749 4748 4750 4751 CONECT 4750 4749 4755 CONECT 4751 4749 4752 4753 CONECT 4752 4751 CONECT 4753 4751 4754 4755 CONECT 4754 4753 CONECT 4755 4750 4753 4756 CONECT 4756 4755 4757 4765 CONECT 4757 4756 4758 CONECT 4758 4757 4759 CONECT 4759 4758 4760 4765 CONECT 4760 4759 4761 4762 CONECT 4761 4760 CONECT 4762 4760 4763 CONECT 4763 4762 4764 CONECT 4764 4763 4765 CONECT 4765 4756 4759 4764 CONECT 4766 1951 4745 CONECT 4767 4768 4769 4770 4774 CONECT 4768 4767 CONECT 4769 4767 CONECT 4770 4767 CONECT 4771 4772 4773 4774 4775 CONECT 4772 4771 CONECT 4773 4771 4794 CONECT 4774 4767 4771 CONECT 4775 4771 4776 CONECT 4776 4775 4777 CONECT 4777 4776 4778 4779 CONECT 4778 4777 4783 CONECT 4779 4777 4780 4781 CONECT 4780 4779 CONECT 4781 4779 4782 4783 CONECT 4782 4781 CONECT 4783 4778 4781 4784 CONECT 4784 4783 4785 4793 CONECT 4785 4784 4786 CONECT 4786 4785 4787 CONECT 4787 4786 4788 4793 CONECT 4788 4787 4789 4790 CONECT 4789 4788 CONECT 4790 4788 4791 CONECT 4791 4790 4792 CONECT 4792 4791 4793 CONECT 4793 4784 4787 4792 CONECT 4794 4773 MASTER 371 0 16 29 26 0 10 6 4987 2 181 50 END