HEADER ISOMERASE 08-DEC-11 3VM6 TITLE CRYSTAL STRUCTURE OF RIBOSE-1,5-BISPHOSPHATE ISOMERASE FROM TITLE 2 THERMOCOCCUS KODAKARENSIS KOD1 IN COMPLEX WITH ALPHA-D-RIBOSE-1,5- TITLE 3 BISPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUNIT; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 5.3.1.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 GENE: E2B2, TK0185; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL-X; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCOLD I KEYWDS ROSSMANN FOLD, HEXAMER, ISOMERASE, AMP METABOLISM, SUGAR BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.NAKAMURA,M.FUJIHASHI,R.AONO,T.SATO,Y.NISHIBA,S.YOSHIDA,A.YANO, AUTHOR 2 H.ATOMI,T.IMANAKA,K.MIKI REVDAT 4 08-NOV-23 3VM6 1 HETSYN REVDAT 3 29-JUL-20 3VM6 1 REMARK SEQADV LINK SITE REVDAT 2 12-JUN-13 3VM6 1 JRNL REVDAT 1 25-APR-12 3VM6 0 JRNL AUTH A.NAKAMURA,M.FUJIHASHI,R.AONO,T.SATO,Y.NISHIBA,S.YOSHIDA, JRNL AUTH 2 A.YANO,H.ATOMI,T.IMANAKA,K.MIKI JRNL TITL DYNAMIC, LIGAND-DEPENDENT CONFORMATIONAL CHANGE TRIGGERS JRNL TITL 2 REACTION OF RIBOSE-1,5-BISPHOSPHATE ISOMERASE FROM JRNL TITL 3 THERMOCOCCUS KODAKARENSIS KOD1 JRNL REF J.BIOL.CHEM. V. 287 20784 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22511789 JRNL DOI 10.1074/JBC.M112.349423 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3065296.180 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25888 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) : 0.201 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1307 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 2.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.03 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4020 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 202 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7635 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 142 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 64.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.72000 REMARK 3 B22 (A**2) : 5.72000 REMARK 3 B33 (A**2) : -11.44000 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) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.35 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) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870 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) : 0.940 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.580 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.480 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.360 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 15.28 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 : LIGANDS.PARAM REMARK 3 PARAMETER FILE 5 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : LIGANDS.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3VM6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000095218. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26012 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12900 REMARK 200 FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.46200 REMARK 200 FOR SHELL : 5.600 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 3A11 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% PEG 1000, 0.2M MAGNESIUM CHLORIDE, REMARK 280 0.1M MES-NAOH PH 6.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.82450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 73.26850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 73.26850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.91225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 73.26850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 73.26850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.73675 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 73.26850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 73.26850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.91225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 73.26850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 73.26850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 74.73675 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.82450 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 29360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 64430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -139.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 MG MG C 413 LIES ON A SPECIAL POSITION. 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 MET A -15 REMARK 465 ASN A -14 REMARK 465 HIS A -13 REMARK 465 LYS A -12 REMARK 465 VAL A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 ILE A -4 REMARK 465 GLU A -3 REMARK 465 GLY A -2 REMARK 465 ARG A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 MET B -15 REMARK 465 ASN B -14 REMARK 465 HIS B -13 REMARK 465 LYS B -12 REMARK 465 VAL B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 ILE B -4 REMARK 465 GLU B -3 REMARK 465 GLY B -2 REMARK 465 ARG B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 MET C -15 REMARK 465 ASN C -14 REMARK 465 HIS C -13 REMARK 465 LYS C -12 REMARK 465 VAL C -11 REMARK 465 HIS C -10 REMARK 465 HIS C -9 REMARK 465 HIS C -8 REMARK 465 HIS C -7 REMARK 465 HIS C -6 REMARK 465 HIS C -5 REMARK 465 ILE C -4 REMARK 465 GLU C -3 REMARK 465 GLY C -2 REMARK 465 ARG C -1 REMARK 465 HIS C 0 REMARK 465 MET C 1 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 ALA A 22 -53.91 -24.20 REMARK 500 GLU A 51 17.69 -66.87 REMARK 500 GLU A 61 33.57 -91.62 REMARK 500 THR A 62 -67.26 -94.43 REMARK 500 ALA A 83 -75.37 -58.08 REMARK 500 SER A 133 -151.16 49.49 REMARK 500 THR A 159 77.01 66.61 REMARK 500 THR A 257 0.36 -64.67 REMARK 500 ALA A 313 -53.19 -26.15 REMARK 500 ASP B 89 -176.77 -67.85 REMARK 500 SER B 133 -153.85 54.59 REMARK 500 THR B 159 85.20 59.68 REMARK 500 GLU B 308 -86.02 -73.45 REMARK 500 LEU B 314 -71.69 -92.59 REMARK 500 PRO B 319 1.97 -66.18 REMARK 500 ALA C 42 126.86 -38.06 REMARK 500 SER C 85 6.01 -68.27 REMARK 500 SER C 133 -164.90 52.37 REMARK 500 THR C 159 77.89 69.43 REMARK 500 LYS C 213 139.51 -38.87 REMARK 500 ASN C 276 75.77 -119.45 REMARK 500 PRO C 319 6.28 -57.01 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 MG A 323 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 304 OD2 REMARK 620 2 ASP B 304 OD2 127.3 REMARK 620 3 ASP C 304 OD2 116.5 114.3 REMARK 620 4 ASP C 304 OD1 87.9 117.4 47.9 REMARK 620 N 1 2 3 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A11 RELATED DB: PDB REMARK 900 UNLIGANDED FORM OF THE SAME PROTEIN REMARK 900 RELATED ID: 3A9C RELATED DB: PDB REMARK 900 RUBP COMPLEX OF THE SAME PROTEIN DBREF 3VM6 A 1 322 UNP Q5JFM9 Q5JFM9_PYRKO 1 322 DBREF 3VM6 B 1 322 UNP Q5JFM9 Q5JFM9_PYRKO 1 322 DBREF 3VM6 C 1 322 UNP Q5JFM9 Q5JFM9_PYRKO 1 322 SEQADV 3VM6 MET A -15 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 ASN A -14 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS A -13 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 LYS A -12 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 VAL A -11 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS A -10 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS A -9 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS A -8 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS A -7 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS A -6 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS A -5 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 ILE A -4 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 GLU A -3 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 GLY A -2 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 ARG A -1 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS A 0 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 SER A 133 UNP Q5JFM9 CYS 133 ENGINEERED MUTATION SEQADV 3VM6 MET B -15 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 ASN B -14 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS B -13 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 LYS B -12 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 VAL B -11 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS B -10 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS B -9 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS B -8 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS B -7 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS B -6 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS B -5 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 ILE B -4 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 GLU B -3 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 GLY B -2 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 ARG B -1 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS B 0 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 SER B 133 UNP Q5JFM9 CYS 133 ENGINEERED MUTATION SEQADV 3VM6 MET C -15 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 ASN C -14 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS C -13 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 LYS C -12 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 VAL C -11 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS C -10 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS C -9 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS C -8 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS C -7 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS C -6 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS C -5 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 ILE C -4 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 GLU C -3 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 GLY C -2 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 ARG C -1 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 HIS C 0 UNP Q5JFM9 EXPRESSION TAG SEQADV 3VM6 SER C 133 UNP Q5JFM9 CYS 133 ENGINEERED MUTATION SEQRES 1 A 338 MET ASN HIS LYS VAL HIS HIS HIS HIS HIS HIS ILE GLU SEQRES 2 A 338 GLY ARG HIS MET ALA VAL VAL LYS GLU VAL LEU GLU ILE SEQRES 3 A 338 ALA GLU LYS ILE LYS ASN MET GLU ILE ARG GLY ALA GLY SEQRES 4 A 338 LYS ILE ALA ARG SER ALA ALA TYR ALA LEU GLN LEU GLN SEQRES 5 A 338 ALA GLU LYS SER LYS ALA THR ASN VAL ASP GLU PHE TRP SEQRES 6 A 338 LYS GLU MET LYS GLN ALA ALA LYS ILE LEU PHE GLU THR SEQRES 7 A 338 ARG PRO THR ALA VAL SER LEU PRO ASN ALA LEU ARG TYR SEQRES 8 A 338 VAL MET HIS ARG GLY LYS ILE ALA TYR SER SER GLY ALA SEQRES 9 A 338 ASP LEU GLU GLN LEU ARG PHE VAL ILE ILE ASN ALA ALA SEQRES 10 A 338 LYS GLU PHE ILE HIS ASN SER GLU LYS ALA LEU GLU ARG SEQRES 11 A 338 ILE GLY GLU PHE GLY ALA LYS ARG ILE GLU ASP GLY ASP SEQRES 12 A 338 VAL ILE MET THR HIS SER HIS SER LYS ALA ALA ILE SER SEQRES 13 A 338 VAL MET LYS THR ALA TRP GLU GLN GLY LYS ASP ILE LYS SEQRES 14 A 338 VAL ILE VAL THR GLU THR ARG PRO LYS TRP GLN GLY LYS SEQRES 15 A 338 ILE THR ALA LYS GLU LEU ALA SER TYR GLY ILE PRO VAL SEQRES 16 A 338 ILE TYR VAL VAL ASP SER ALA ALA ARG HIS TYR MET LYS SEQRES 17 A 338 MET THR ASP LYS VAL VAL MET GLY ALA ASP SER ILE THR SEQRES 18 A 338 VAL ASN GLY ALA VAL ILE ASN LYS ILE GLY THR ALA LEU SEQRES 19 A 338 ILE ALA LEU THR ALA LYS GLU HIS ARG VAL TRP THR MET SEQRES 20 A 338 ILE ALA ALA GLU THR TYR LYS PHE HIS PRO GLU THR MET SEQRES 21 A 338 LEU GLY GLN LEU VAL GLU ILE GLU MET ARG ASP PRO THR SEQRES 22 A 338 GLU VAL ILE PRO GLU ASP GLU LEU LYS THR TRP PRO LYS SEQRES 23 A 338 ASN ILE GLU VAL TRP ASN PRO ALA PHE ASP VAL THR PRO SEQRES 24 A 338 PRO GLU TYR VAL ASP VAL ILE ILE THR GLU ARG GLY ILE SEQRES 25 A 338 ILE PRO PRO TYR ALA ALA ILE ASP ILE LEU ARG GLU GLU SEQRES 26 A 338 PHE GLY TRP ALA LEU LYS TYR THR GLU PRO TRP GLU ASP SEQRES 1 B 338 MET ASN HIS LYS VAL HIS HIS HIS HIS HIS HIS ILE GLU SEQRES 2 B 338 GLY ARG HIS MET ALA VAL VAL LYS GLU VAL LEU GLU ILE SEQRES 3 B 338 ALA GLU LYS ILE LYS ASN MET GLU ILE ARG GLY ALA GLY SEQRES 4 B 338 LYS ILE ALA ARG SER ALA ALA TYR ALA LEU GLN LEU GLN SEQRES 5 B 338 ALA GLU LYS SER LYS ALA THR ASN VAL ASP GLU PHE TRP SEQRES 6 B 338 LYS GLU MET LYS GLN ALA ALA LYS ILE LEU PHE GLU THR SEQRES 7 B 338 ARG PRO THR ALA VAL SER LEU PRO ASN ALA LEU ARG TYR SEQRES 8 B 338 VAL MET HIS ARG GLY LYS ILE ALA TYR SER SER GLY ALA SEQRES 9 B 338 ASP LEU GLU GLN LEU ARG PHE VAL ILE ILE ASN ALA ALA SEQRES 10 B 338 LYS GLU PHE ILE HIS ASN SER GLU LYS ALA LEU GLU ARG SEQRES 11 B 338 ILE GLY GLU PHE GLY ALA LYS ARG ILE GLU ASP GLY ASP SEQRES 12 B 338 VAL ILE MET THR HIS SER HIS SER LYS ALA ALA ILE SER SEQRES 13 B 338 VAL MET LYS THR ALA TRP GLU GLN GLY LYS ASP ILE LYS SEQRES 14 B 338 VAL ILE VAL THR GLU THR ARG PRO LYS TRP GLN GLY LYS SEQRES 15 B 338 ILE THR ALA LYS GLU LEU ALA SER TYR GLY ILE PRO VAL SEQRES 16 B 338 ILE TYR VAL VAL ASP SER ALA ALA ARG HIS TYR MET LYS SEQRES 17 B 338 MET THR ASP LYS VAL VAL MET GLY ALA ASP SER ILE THR SEQRES 18 B 338 VAL ASN GLY ALA VAL ILE ASN LYS ILE GLY THR ALA LEU SEQRES 19 B 338 ILE ALA LEU THR ALA LYS GLU HIS ARG VAL TRP THR MET SEQRES 20 B 338 ILE ALA ALA GLU THR TYR LYS PHE HIS PRO GLU THR MET SEQRES 21 B 338 LEU GLY GLN LEU VAL GLU ILE GLU MET ARG ASP PRO THR SEQRES 22 B 338 GLU VAL ILE PRO GLU ASP GLU LEU LYS THR TRP PRO LYS SEQRES 23 B 338 ASN ILE GLU VAL TRP ASN PRO ALA PHE ASP VAL THR PRO SEQRES 24 B 338 PRO GLU TYR VAL ASP VAL ILE ILE THR GLU ARG GLY ILE SEQRES 25 B 338 ILE PRO PRO TYR ALA ALA ILE ASP ILE LEU ARG GLU GLU SEQRES 26 B 338 PHE GLY TRP ALA LEU LYS TYR THR GLU PRO TRP GLU ASP SEQRES 1 C 338 MET ASN HIS LYS VAL HIS HIS HIS HIS HIS HIS ILE GLU SEQRES 2 C 338 GLY ARG HIS MET ALA VAL VAL LYS GLU VAL LEU GLU ILE SEQRES 3 C 338 ALA GLU LYS ILE LYS ASN MET GLU ILE ARG GLY ALA GLY SEQRES 4 C 338 LYS ILE ALA ARG SER ALA ALA TYR ALA LEU GLN LEU GLN SEQRES 5 C 338 ALA GLU LYS SER LYS ALA THR ASN VAL ASP GLU PHE TRP SEQRES 6 C 338 LYS GLU MET LYS GLN ALA ALA LYS ILE LEU PHE GLU THR SEQRES 7 C 338 ARG PRO THR ALA VAL SER LEU PRO ASN ALA LEU ARG TYR SEQRES 8 C 338 VAL MET HIS ARG GLY LYS ILE ALA TYR SER SER GLY ALA SEQRES 9 C 338 ASP LEU GLU GLN LEU ARG PHE VAL ILE ILE ASN ALA ALA SEQRES 10 C 338 LYS GLU PHE ILE HIS ASN SER GLU LYS ALA LEU GLU ARG SEQRES 11 C 338 ILE GLY GLU PHE GLY ALA LYS ARG ILE GLU ASP GLY ASP SEQRES 12 C 338 VAL ILE MET THR HIS SER HIS SER LYS ALA ALA ILE SER SEQRES 13 C 338 VAL MET LYS THR ALA TRP GLU GLN GLY LYS ASP ILE LYS SEQRES 14 C 338 VAL ILE VAL THR GLU THR ARG PRO LYS TRP GLN GLY LYS SEQRES 15 C 338 ILE THR ALA LYS GLU LEU ALA SER TYR GLY ILE PRO VAL SEQRES 16 C 338 ILE TYR VAL VAL ASP SER ALA ALA ARG HIS TYR MET LYS SEQRES 17 C 338 MET THR ASP LYS VAL VAL MET GLY ALA ASP SER ILE THR SEQRES 18 C 338 VAL ASN GLY ALA VAL ILE ASN LYS ILE GLY THR ALA LEU SEQRES 19 C 338 ILE ALA LEU THR ALA LYS GLU HIS ARG VAL TRP THR MET SEQRES 20 C 338 ILE ALA ALA GLU THR TYR LYS PHE HIS PRO GLU THR MET SEQRES 21 C 338 LEU GLY GLN LEU VAL GLU ILE GLU MET ARG ASP PRO THR SEQRES 22 C 338 GLU VAL ILE PRO GLU ASP GLU LEU LYS THR TRP PRO LYS SEQRES 23 C 338 ASN ILE GLU VAL TRP ASN PRO ALA PHE ASP VAL THR PRO SEQRES 24 C 338 PRO GLU TYR VAL ASP VAL ILE ILE THR GLU ARG GLY ILE SEQRES 25 C 338 ILE PRO PRO TYR ALA ALA ILE ASP ILE LEU ARG GLU GLU SEQRES 26 C 338 PHE GLY TRP ALA LEU LYS TYR THR GLU PRO TRP GLU ASP HET RI2 A 401 18 HET PEG A 402 7 HET PEG A 403 7 HET PEG A 404 7 HET CL A 411 1 HET MG A 323 1 HET RI2 B 401 18 HET PEG B 402 7 HET PG4 B 403 13 HET PEG B 404 7 HET PEG B 405 7 HET CL B 411 1 HET RI2 C 401 18 HET PEG C 402 7 HET PEG C 403 7 HET PEG C 404 7 HET PEG C 405 7 HET CL C 412 1 HET MG C 413 1 HETNAM RI2 1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM PG4 TETRAETHYLENE GLYCOL HETSYN RI2 1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOSE; 1,5-DI-O-PHOSPHONO- HETSYN 2 RI2 D-RIBOSE; 1,5-DI-O-PHOSPHONO-RIBOSE FORMUL 4 RI2 3(C5 H12 O11 P2) FORMUL 5 PEG 10(C4 H10 O3) FORMUL 8 CL 3(CL 1-) FORMUL 9 MG 2(MG 2+) FORMUL 12 PG4 C8 H18 O5 FORMUL 23 HOH *153(H2 O) HELIX 1 1 LYS A 5 ASN A 16 1 12 HELIX 2 2 ALA A 22 LYS A 39 1 18 HELIX 3 3 VAL A 45 GLU A 61 1 17 HELIX 4 4 VAL A 67 SER A 86 1 20 HELIX 5 5 LEU A 90 ARG A 122 1 33 HELIX 6 6 LYS A 136 GLN A 148 1 13 HELIX 7 7 GLN A 164 TYR A 175 1 12 HELIX 8 8 ASP A 184 HIS A 189 5 6 HELIX 9 9 TYR A 190 MET A 193 5 4 HELIX 10 10 THR A 216 HIS A 226 1 11 HELIX 11 11 THR A 236 LYS A 238 5 3 HELIX 12 12 PRO A 256 VAL A 259 5 4 HELIX 13 13 GLU A 262 THR A 267 1 6 HELIX 14 14 PRO A 284 TYR A 286 5 3 HELIX 15 15 ALA A 302 GLU A 309 1 8 HELIX 16 1 LYS B 5 ASN B 16 1 12 HELIX 17 2 ALA B 22 LYS B 39 1 18 HELIX 18 3 VAL B 45 GLU B 61 1 17 HELIX 19 4 VAL B 67 SER B 86 1 20 HELIX 20 5 LEU B 90 ARG B 122 1 33 HELIX 21 6 LYS B 136 GLN B 148 1 13 HELIX 22 7 GLN B 164 TYR B 175 1 12 HELIX 23 8 ASP B 184 HIS B 189 5 6 HELIX 24 9 TYR B 190 MET B 193 5 4 HELIX 25 10 THR B 216 HIS B 226 1 11 HELIX 26 11 THR B 236 LYS B 238 5 3 HELIX 27 12 PRO B 256 VAL B 259 5 4 HELIX 28 13 GLU B 262 THR B 267 1 6 HELIX 29 14 PRO B 284 TYR B 286 5 3 HELIX 30 15 ALA B 302 GLU B 309 1 8 HELIX 31 1 LYS C 5 ASN C 16 1 12 HELIX 32 2 ALA C 22 LYS C 39 1 18 HELIX 33 3 VAL C 45 GLU C 61 1 17 HELIX 34 4 VAL C 67 SER C 86 1 20 HELIX 35 5 LEU C 90 ARG C 122 1 33 HELIX 36 6 LYS C 136 GLN C 148 1 13 HELIX 37 7 GLN C 164 TYR C 175 1 12 HELIX 38 8 ASP C 184 HIS C 189 5 6 HELIX 39 9 TYR C 190 MET C 193 5 4 HELIX 40 10 THR C 216 HIS C 226 1 11 HELIX 41 11 THR C 236 LYS C 238 5 3 HELIX 42 12 PRO C 256 VAL C 259 5 4 HELIX 43 13 GLU C 262 THR C 267 1 6 HELIX 44 14 PRO C 284 TYR C 286 5 3 HELIX 45 15 ALA C 302 GLU C 309 1 8 SHEET 1 A 7 VAL A 179 VAL A 182 0 SHEET 2 A 7 LYS A 153 THR A 157 1 N VAL A 154 O ILE A 180 SHEET 3 A 7 VAL A 128 THR A 131 1 N ILE A 129 O ILE A 155 SHEET 4 A 7 LYS A 196 MET A 199 1 O LYS A 196 N MET A 130 SHEET 5 A 7 THR A 230 ALA A 234 1 O MET A 231 N VAL A 197 SHEET 6 A 7 VAL A 289 ILE A 291 1 O ILE A 291 N ILE A 232 SHEET 7 A 7 GLY A 295 ILE A 297 -1 O ILE A 297 N ILE A 290 SHEET 1 B 3 ASP A 202 THR A 205 0 SHEET 2 B 3 ALA A 209 LYS A 213 -1 O ILE A 211 N SER A 203 SHEET 3 B 3 PHE A 279 THR A 282 -1 O THR A 282 N VAL A 210 SHEET 1 C 7 VAL B 179 VAL B 182 0 SHEET 2 C 7 LYS B 153 THR B 157 1 N VAL B 154 O ILE B 180 SHEET 3 C 7 VAL B 128 THR B 131 1 N ILE B 129 O ILE B 155 SHEET 4 C 7 LYS B 196 MET B 199 1 O LYS B 196 N MET B 130 SHEET 5 C 7 THR B 230 ALA B 234 1 O MET B 231 N VAL B 197 SHEET 6 C 7 VAL B 289 ILE B 291 1 O ILE B 291 N ILE B 232 SHEET 7 C 7 GLY B 295 ILE B 297 -1 O ILE B 297 N ILE B 290 SHEET 1 D 3 ASP B 202 THR B 205 0 SHEET 2 D 3 ALA B 209 LYS B 213 -1 O ILE B 211 N SER B 203 SHEET 3 D 3 PHE B 279 THR B 282 -1 O THR B 282 N VAL B 210 SHEET 1 E 7 VAL C 179 VAL C 182 0 SHEET 2 E 7 LYS C 153 THR C 157 1 N VAL C 154 O ILE C 180 SHEET 3 E 7 VAL C 128 THR C 131 1 N ILE C 129 O ILE C 155 SHEET 4 E 7 LYS C 196 MET C 199 1 O LYS C 196 N MET C 130 SHEET 5 E 7 THR C 230 ALA C 234 1 O MET C 231 N VAL C 197 SHEET 6 E 7 VAL C 289 ILE C 291 1 O ILE C 291 N ILE C 232 SHEET 7 E 7 GLY C 295 ILE C 297 -1 O ILE C 297 N ILE C 290 SHEET 1 F 3 ASP C 202 THR C 205 0 SHEET 2 F 3 ALA C 209 LYS C 213 -1 O ILE C 211 N SER C 203 SHEET 3 F 3 PHE C 279 THR C 282 -1 O THR C 282 N VAL C 210 LINK OD2 ASP A 304 MG MG A 323 1555 1555 2.88 LINK MG MG A 323 OD2 ASP B 304 1555 1555 2.67 LINK MG MG A 323 OD2 ASP C 304 1555 1555 2.61 LINK MG MG A 323 OD1 ASP C 304 1555 1555 2.79 LINK O LYS C 192 MG MG C 413 1555 1555 2.93 CISPEP 1 ARG A 160 PRO A 161 0 1.23 CISPEP 2 ARG B 160 PRO B 161 0 0.00 CISPEP 3 ARG C 160 PRO C 161 0 0.67 CRYST1 146.537 146.537 99.649 90.00 90.00 90.00 P 41 21 2 24 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 0.006824 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006824 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010035 0.00000