HEADER LIGASE 23-APR-07 2YWV TITLE CRYSTAL STRUCTURE OF SAICAR SYNTHETASE FROM GEOBACILLUS KAUSTOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHORIBOSYLAMINOIMIDAZOLE SUCCINOCARBOXAMIDE SYNTHETASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 6.3.2.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS KAUSTOPHILUS; SOURCE 3 ORGANISM_TAXID: 1462; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-HISTEV KEYWDS ADP COMPLEX, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 2 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KANAGAWA,S.BABA,S.KURAMITSU,S.YOKOYAMA,G.KAWAI,G.SAMPEI,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 25-OCT-23 2YWV 1 REMARK SEQADV REVDAT 3 13-JUL-11 2YWV 1 VERSN REVDAT 2 24-FEB-09 2YWV 1 VERSN REVDAT 1 23-OCT-07 2YWV 0 JRNL AUTH M.KANAGAWA,S.BABA,S.KURAMITSU,S.YOKOYAMA,G.KAWAI,G.SAMPEI JRNL TITL CRYSTAL STRUCTURE OF SAICAR SYNTHETASE FROM GEOBACILLUS JRNL TITL 2 KAUSTOPHILUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 233767.800 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 46761 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) : 0.188 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4714 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6193 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 684 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.009 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3754 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 91 REMARK 3 SOLVENT ATOMS : 525 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.46000 REMARK 3 B22 (A**2) : -1.63000 REMARK 3 B33 (A**2) : -0.83000 REMARK 3 B12 (A**2) : 1.18000 REMARK 3 B13 (A**2) : 1.19000 REMARK 3 B23 (A**2) : -2.31000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 2.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.920 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.100 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.700 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.950 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.880 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 62.89 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 : LIGAND.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : LIGAND.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YWV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000027235. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : FIXED EXIT SI DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92845 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 1.500 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.11800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2GQS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 ACETATE TRIHYDRATE(PH4.6), 30%W/V PEG MME 2000 , VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 APPLY THE FOLLOWING TO CHAINS: A, 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -148.0 KCAL/MOL 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 1.06782 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -53.84312 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -50.76656 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 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 GLY A -1 REMARK 465 HIS A 0 REMARK 465 SER A 238 REMARK 465 ALA A 239 REMARK 465 CYS A 240 REMARK 465 THR A 241 REMARK 465 LYS A 242 REMARK 465 GLY B -1 REMARK 465 HIS B 0 REMARK 465 SER B 238 REMARK 465 ALA B 239 REMARK 465 CYS B 240 REMARK 465 THR B 241 REMARK 465 LYS B 242 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2 GLN A 154 O HOH A 874 1.33 REMARK 500 OE2 GLU B 237 O HOH B 839 1.55 REMARK 500 OE1 GLU B 53 O HOH B 855 1.80 REMARK 500 O3 SO4 B 546 O HOH B 799 1.88 REMARK 500 NZ LYS A 74 O HOH A 910 1.89 REMARK 500 NZ LYS B 74 O HOH B 828 1.98 REMARK 500 NH1 ARG B 164 O HOH B 962 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 MET A 1 CA - C - N ANGL. DEV. = 19.3 DEGREES REMARK 500 MET A 1 O - C - N ANGL. DEV. = -17.9 DEGREES REMARK 500 PRO A 2 CA - C - N ANGL. DEV. = -26.4 DEGREES REMARK 500 PRO A 2 O - C - N ANGL. DEV. = 24.2 DEGREES REMARK 500 THR A 3 C - N - CA ANGL. DEV. = -24.4 DEGREES REMARK 500 LYS A 12 CA - CB - CG ANGL. DEV. = 58.4 DEGREES REMARK 500 LYS A 14 CG - CD - CE ANGL. DEV. = 32.2 DEGREES REMARK 500 LYS A 41 CA - CB - CG ANGL. DEV. = 45.1 DEGREES REMARK 500 GLU A 115 CA - CB - CG ANGL. DEV. = -24.7 DEGREES REMARK 500 ALA A 192 CA - C - N ANGL. DEV. = 23.1 DEGREES REMARK 500 ALA A 192 O - C - N ANGL. DEV. = -24.5 DEGREES REMARK 500 ASP A 193 C - N - CA ANGL. DEV. = 44.7 DEGREES REMARK 500 ASP A 193 CB - CA - C ANGL. DEV. = 23.1 DEGREES REMARK 500 ASP A 193 N - CA - C ANGL. DEV. = -23.1 DEGREES REMARK 500 ASP A 193 CA - C - N ANGL. DEV. = -19.2 DEGREES REMARK 500 PRO B 2 C - N - CA ANGL. DEV. = -16.5 DEGREES REMARK 500 PRO B 2 CB - CA - C ANGL. DEV. = 35.4 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 GLN A 5 -143.44 -113.74 REMARK 500 ASP A 31 53.05 -95.76 REMARK 500 PRO A 89 56.01 -65.85 REMARK 500 ALA A 192 -159.11 -128.16 REMARK 500 ASP A 193 -124.73 66.34 REMARK 500 GLN B 5 -142.37 -113.91 REMARK 500 ASP B 31 53.30 -93.48 REMARK 500 PRO B 89 57.34 -66.86 REMARK 500 ALA B 192 -152.28 -131.80 REMARK 500 ASP B 193 -126.87 59.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET A 1 PRO A 2 142.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 83 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 MET A 1 -21.25 REMARK 500 ASP A 193 13.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 541 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 542 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 543 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 544 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 545 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 546 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 548 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GKA001000260.1 RELATED DB: TARGETDB DBREF 2YWV A 1 242 UNP Q5L3D5 Q5L3D5_GEOKA 1 242 DBREF 2YWV B 1 242 UNP Q5L3D5 Q5L3D5_GEOKA 1 242 SEQADV 2YWV GLY A -1 UNP Q5L3D5 EXPRESSION TAG SEQADV 2YWV HIS A 0 UNP Q5L3D5 EXPRESSION TAG SEQADV 2YWV GLY B -1 UNP Q5L3D5 EXPRESSION TAG SEQADV 2YWV HIS B 0 UNP Q5L3D5 EXPRESSION TAG SEQRES 1 A 244 GLY HIS MET PRO THR LYS GLN GLN LEU LEU TYR GLU GLY SEQRES 2 A 244 LYS ALA LYS LYS ILE TYR ALA THR ASP GLU PRO ASP VAL SEQRES 3 A 244 LEU TRP VAL GLU TYR LYS ASP SER ALA THR ALA PHE ASN SEQRES 4 A 244 GLY GLU LYS LYS ALA THR ILE ALA GLY LYS GLY ARG LEU SEQRES 5 A 244 ASN ASN GLU ILE SER SER LEU LEU PHE LEU LYS LEU ARG SEQRES 6 A 244 GLU ALA GLY ILE ALA ASN HIS PHE ILE GLU LYS LEU SER SEQRES 7 A 244 PRO THR GLU GLN LEU VAL ARG ARG VAL THR ILE ILE PRO SEQRES 8 A 244 LEU GLU VAL VAL VAL ARG ASN VAL VAL ALA GLY SER LEU SEQRES 9 A 244 ALA LYS ARG ILE GLY LEU GLU GLU GLY THR PRO LEU GLU SEQRES 10 A 244 ALA PRO LEU VAL GLU PHE TYR TYR LYS ASN ASP ASP LEU SEQRES 11 A 244 GLY ASP PRO LEU LEU LEU GLU ASP HIS ILE PHE ILE LEU SEQRES 12 A 244 LYS LEU ALA SER ARG GLU GLU VAL ALA ALA LEU LYS GLN SEQRES 13 A 244 ALA ALA LEU ALA VAL ASN ASP VAL LEU ARG LEU HIS PHE SEQRES 14 A 244 ALA GLU ARG ASN VAL ARG LEU ILE ASP PHE LYS LEU GLU SEQRES 15 A 244 PHE GLY ARG THR ALA ASP GLY ALA ILE LEU LEU ALA ASP SEQRES 16 A 244 GLU ILE SER PRO ASP THR CYS ARG LEU TRP ASP ALA LYS SEQRES 17 A 244 THR ASN GLU LYS LEU ASP LYS ASP VAL PHE ARG ARG ASP SEQRES 18 A 244 LEU GLY SER LEU THR ASP ALA TYR GLU VAL ILE LEU GLN SEQRES 19 A 244 ARG LEU GLY GLY GLU SER ALA CYS THR LYS SEQRES 1 B 244 GLY HIS MET PRO THR LYS GLN GLN LEU LEU TYR GLU GLY SEQRES 2 B 244 LYS ALA LYS LYS ILE TYR ALA THR ASP GLU PRO ASP VAL SEQRES 3 B 244 LEU TRP VAL GLU TYR LYS ASP SER ALA THR ALA PHE ASN SEQRES 4 B 244 GLY GLU LYS LYS ALA THR ILE ALA GLY LYS GLY ARG LEU SEQRES 5 B 244 ASN ASN GLU ILE SER SER LEU LEU PHE LEU LYS LEU ARG SEQRES 6 B 244 GLU ALA GLY ILE ALA ASN HIS PHE ILE GLU LYS LEU SER SEQRES 7 B 244 PRO THR GLU GLN LEU VAL ARG ARG VAL THR ILE ILE PRO SEQRES 8 B 244 LEU GLU VAL VAL VAL ARG ASN VAL VAL ALA GLY SER LEU SEQRES 9 B 244 ALA LYS ARG ILE GLY LEU GLU GLU GLY THR PRO LEU GLU SEQRES 10 B 244 ALA PRO LEU VAL GLU PHE TYR TYR LYS ASN ASP ASP LEU SEQRES 11 B 244 GLY ASP PRO LEU LEU LEU GLU ASP HIS ILE PHE ILE LEU SEQRES 12 B 244 LYS LEU ALA SER ARG GLU GLU VAL ALA ALA LEU LYS GLN SEQRES 13 B 244 ALA ALA LEU ALA VAL ASN ASP VAL LEU ARG LEU HIS PHE SEQRES 14 B 244 ALA GLU ARG ASN VAL ARG LEU ILE ASP PHE LYS LEU GLU SEQRES 15 B 244 PHE GLY ARG THR ALA ASP GLY ALA ILE LEU LEU ALA ASP SEQRES 16 B 244 GLU ILE SER PRO ASP THR CYS ARG LEU TRP ASP ALA LYS SEQRES 17 B 244 THR ASN GLU LYS LEU ASP LYS ASP VAL PHE ARG ARG ASP SEQRES 18 B 244 LEU GLY SER LEU THR ASP ALA TYR GLU VAL ILE LEU GLN SEQRES 19 B 244 ARG LEU GLY GLY GLU SER ALA CYS THR LYS HET SO4 A 543 5 HET SO4 A 544 5 HET SO4 A 545 5 HET MG A 701 1 HET ADP A 600 27 HET SO4 B 541 5 HET SO4 B 542 5 HET SO4 B 546 5 HET SO4 B 548 5 HET MG B 702 1 HET ADP B 601 27 HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 3 SO4 7(O4 S 2-) FORMUL 6 MG 2(MG 2+) FORMUL 7 ADP 2(C10 H15 N5 O10 P2) FORMUL 14 HOH *525(H2 O) HELIX 1 1 GLY A 46 ALA A 65 1 20 HELIX 2 2 ALA A 99 GLY A 107 1 9 HELIX 3 3 ASN A 125 GLY A 129 5 5 HELIX 4 4 LEU A 134 LYS A 142 1 9 HELIX 5 5 SER A 145 ARG A 170 1 26 HELIX 6 6 LYS A 213 ARG A 218 1 6 HELIX 7 7 SER A 222 LEU A 234 1 13 HELIX 8 8 GLY B 46 ALA B 65 1 20 HELIX 9 9 ALA B 99 GLY B 107 1 9 HELIX 10 10 ASN B 125 GLY B 129 5 5 HELIX 11 11 LEU B 134 LYS B 142 1 9 HELIX 12 12 SER B 145 GLU B 169 1 25 HELIX 13 13 LYS B 213 ARG B 218 1 6 HELIX 14 14 SER B 222 LEU B 234 1 13 SHEET 1 A 5 LYS A 4 GLU A 10 0 SHEET 2 A 5 LYS A 14 THR A 19 -1 O ILE A 16 N TYR A 9 SHEET 3 A 5 VAL A 24 TYR A 29 -1 O TRP A 26 N TYR A 17 SHEET 4 A 5 GLU A 79 ARG A 83 -1 O VAL A 82 N LEU A 25 SHEET 5 A 5 PHE A 71 LYS A 74 -1 N GLU A 73 O LEU A 81 SHEET 1 B 2 SER A 32 ALA A 35 0 SHEET 2 B 2 LYS A 40 THR A 43 -1 O LYS A 40 N ALA A 35 SHEET 1 C 3 THR A 86 ILE A 87 0 SHEET 2 C 3 PHE A 181 ARG A 183 -1 O ARG A 183 N THR A 86 SHEET 3 C 3 ILE A 189 LEU A 191 -1 O LEU A 190 N GLY A 182 SHEET 1 D 5 LEU A 132 LEU A 133 0 SHEET 2 D 5 THR A 112 TYR A 123 -1 N PHE A 121 O LEU A 133 SHEET 3 D 5 LEU A 90 VAL A 98 -1 N GLU A 91 O TYR A 122 SHEET 4 D 5 VAL A 172 LEU A 179 -1 O LEU A 179 N VAL A 92 SHEET 5 D 5 CYS A 200 ASP A 204 -1 O TRP A 203 N ARG A 173 SHEET 1 E 5 LYS B 4 GLU B 10 0 SHEET 2 E 5 LYS B 14 THR B 19 -1 O ILE B 16 N TYR B 9 SHEET 3 E 5 VAL B 24 TYR B 29 -1 O TRP B 26 N TYR B 17 SHEET 4 E 5 GLU B 79 ARG B 83 -1 O VAL B 82 N LEU B 25 SHEET 5 E 5 PHE B 71 LYS B 74 -1 N GLU B 73 O LEU B 81 SHEET 1 F 2 SER B 32 ALA B 35 0 SHEET 2 F 2 LYS B 40 THR B 43 -1 O ALA B 42 N ALA B 33 SHEET 1 G 3 THR B 86 ILE B 87 0 SHEET 2 G 3 VAL B 172 ARG B 183 -1 O ARG B 183 N THR B 86 SHEET 3 G 3 ILE B 189 ALA B 192 -1 O ALA B 192 N GLU B 180 SHEET 1 H 5 LEU B 132 LEU B 133 0 SHEET 2 H 5 PRO B 113 TYR B 123 -1 N PHE B 121 O LEU B 133 SHEET 3 H 5 LEU B 90 VAL B 97 -1 N VAL B 93 O GLU B 120 SHEET 4 H 5 VAL B 172 ARG B 183 -1 O LEU B 179 N VAL B 92 SHEET 5 H 5 CYS B 200 ASP B 204 -1 O TRP B 203 N ARG B 173 SITE 1 AC1 7 ARG B 95 GLY B 100 SER B 101 ARG B 201 SITE 2 AC1 7 HOH B 823 HOH B 901 HOH B 914 SITE 1 AC2 7 ALA B 35 PHE B 36 ASN B 37 LYS B 213 SITE 2 AC2 7 ARG B 217 HOH B 881 HOH B 912 SITE 1 AC3 7 ARG A 95 GLY A 100 SER A 101 ARG A 201 SITE 2 AC3 7 HOH A 807 HOH A 821 HOH A 904 SITE 1 AC4 6 ALA A 35 PHE A 36 ASN A 37 LYS A 213 SITE 2 AC4 6 ARG A 217 HOH A 858 SITE 1 AC5 6 VAL A 97 ARG A 164 ARG A 173 HOH A 793 SITE 2 AC5 6 HOH A 826 HOH A 957 SITE 1 AC6 5 VAL B 97 ARG B 173 HOH B 779 HOH B 799 SITE 2 AC6 5 HOH B 820 SITE 1 AC7 6 ARG A 105 PRO A 131 LEU A 132 ARG B 105 SITE 2 AC7 6 HOH B 782 HOH B 933 SITE 1 AC8 6 ASP A 193 ADP A 600 HOH A 706 HOH A 709 SITE 2 AC8 6 HOH A 787 HOH A 798 SITE 1 AC9 5 ADP B 601 HOH B 708 HOH B 709 HOH B 713 SITE 2 AC9 5 HOH B 812 SITE 1 BC1 18 TYR A 9 GLY A 11 LYS A 12 ALA A 13 SITE 2 BC1 18 LYS A 14 ILE A 16 LEU A 25 HIS A 70 SITE 3 BC1 18 ARG A 83 VAL A 85 ILE A 87 LYS A 124 SITE 4 BC1 18 GLU A 180 ASP A 193 MG A 701 HOH A 706 SITE 5 BC1 18 HOH A 833 HOH A 862 SITE 1 BC2 18 TYR B 9 GLY B 11 LYS B 12 ALA B 13 SITE 2 BC2 18 LYS B 14 ILE B 16 LEU B 25 HIS B 70 SITE 3 BC2 18 ARG B 83 VAL B 85 ILE B 87 LYS B 124 SITE 4 BC2 18 GLU B 180 ASP B 193 MG B 702 HOH B 708 SITE 5 BC2 18 HOH B 735 HOH B 877 CRYST1 49.890 56.397 56.410 76.39 64.36 64.35 P 1 2 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 0.020044 -0.009625 -0.009068 0.00000 SCALE2 0.000000 0.019670 -0.001164 0.00000 SCALE3 0.000000 0.000000 0.019698 0.00000