HEADER LYASE 08-OCT-08 3ETJ TITLE CRYSTAL STRUCTURE E. COLI PURK IN COMPLEX WITH MG, ADP, AND PI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE ATPASE SUBUNIT; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: AIR CARBOXYLASE, AIRC; COMPND 5 EC: 4.1.1.21; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B0522, JW0511, PURK, PURK_ECOLI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HMS174(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET31 KEYWDS ATP-GRASP, PURINE BIOSYNTHESIS, ANTIMICROBIAL, ATP-BINDING, KEYWDS 2 DECARBOXYLASE, LYASE, NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR H.M.HOLDEN,J.B.THODEN REVDAT 6 06-SEP-23 3ETJ 1 REMARK REVDAT 5 20-OCT-21 3ETJ 1 REMARK SEQADV LINK REVDAT 4 09-JUN-09 3ETJ 1 REVDAT REVDAT 3 24-FEB-09 3ETJ 1 VERSN REVDAT 2 30-DEC-08 3ETJ 1 JRNL REVDAT 1 21-OCT-08 3ETJ 0 JRNL AUTH J.B.THODEN,H.M.HOLDEN,S.M.FIRESTINE JRNL TITL STRUCTURAL ANALYSIS OF THE ACTIVE SITE GEOMETRY OF JRNL TITL 2 N(5)-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE FROM JRNL TITL 3 ESCHERICHIA COLI. JRNL REF BIOCHEMISTRY V. 47 13346 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 19053251 JRNL DOI 10.1021/BI801734Z REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 80952 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 6164 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1600 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 80952 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5537 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 69 REMARK 3 SOLVENT ATOMS : 681 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : NULL ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : ENGH & HUBER REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3ETJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000049748. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80957 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.20700 REMARK 200 R SYM FOR SHELL (I) : 0.20700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3ETH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MONOMETHYLETHER POLY(ETHYLENE GLYCOL) REMARK 280 5000, MGATP, 5-AMINOIMIDAZOLE RIBONUCLEOTIDE, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 64.40000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 64.40000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.25000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -88.0 KCAL/MOL 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 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 TYR B 126 REMARK 465 ASP B 127 REMARK 465 GLY B 128 REMARK 465 ARG B 129 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 OG SER B 326 O HOH B 653 2.12 REMARK 500 OD1 ASP A 324 OG SER A 326 2.15 REMARK 500 O HOH A 656 O HOH A 779 2.16 REMARK 500 OH TYR A 126 NH1 ARG A 129 2.16 REMARK 500 O GLU B 308 NH1 ARG B 313 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 GLN A 215 O HOH B 681 3445 2.15 REMARK 500 NH1 ARG B 135 O HOH A 698 4546 2.16 REMARK 500 O HOH B 646 O HOH B 646 2657 2.17 REMARK 500 O HOH A 753 O HOH A 753 2557 2.19 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 ARG A 60 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 80 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 LEU A 81 CB - CG - CD1 ANGL. DEV. = -13.3 DEGREES REMARK 500 LEU A 99 CB - CG - CD1 ANGL. DEV. = -12.7 DEGREES REMARK 500 ARG A 133 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 VAL A 162 CG1 - CB - CG2 ANGL. DEV. = 10.2 DEGREES REMARK 500 GLN A 197 CB - CA - C ANGL. DEV. = -12.3 DEGREES REMARK 500 LEU A 235 CB - CG - CD2 ANGL. DEV. = -15.2 DEGREES REMARK 500 ARG A 264 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 LEU A 269 CB - CG - CD1 ANGL. DEV. = 14.0 DEGREES REMARK 500 LEU A 320 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 LEU A 320 CB - CG - CD2 ANGL. DEV. = -19.4 DEGREES REMARK 500 ARG A 327 CB - CA - C ANGL. DEV. = -13.0 DEGREES REMARK 500 MET B 1 CA - CB - CG ANGL. DEV. = 10.6 DEGREES REMARK 500 ARG B 17 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 PHE B 41 CB - CA - C ANGL. DEV. = 13.6 DEGREES REMARK 500 VAL B 45 N - CA - C ANGL. DEV. = -20.0 DEGREES REMARK 500 ARG B 80 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 103 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 103 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 TRP B 106 N - CA - C ANGL. DEV. = 17.2 DEGREES REMARK 500 ARG B 133 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 242 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG B 242 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 264 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 LEU B 299 CB - CG - CD1 ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG B 313 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP B 322 CB - CG - OD2 ANGL. DEV. = 7.2 DEGREES REMARK 500 LEU B 339 CB - CG - CD2 ANGL. DEV. = -10.7 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 PRO A 40 41.22 -74.86 REMARK 500 ASP A 127 15.63 58.11 REMARK 500 ASN A 237 -65.18 -91.21 REMARK 500 ARG A 242 176.24 176.64 REMARK 500 ALA B 38 11.06 -61.56 REMARK 500 PRO B 40 46.12 -64.92 REMARK 500 ARG B 242 174.50 173.84 REMARK 500 ASP B 322 147.36 -174.14 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 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 226 OE2 REMARK 620 2 GLU A 238 OE1 76.9 REMARK 620 3 ADP A 400 O2B 170.1 96.2 REMARK 620 4 ADP A 400 O2A 103.0 87.0 83.5 REMARK 620 5 PI A 403 O2 94.4 84.0 77.7 158.1 REMARK 620 6 HOH A 694 O 104.6 178.3 82.5 91.8 96.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 238 OE1 REMARK 620 2 GLU A 238 OE2 55.7 REMARK 620 3 ADP A 400 O1B 92.2 83.4 REMARK 620 4 PI A 403 O1 96.4 152.0 101.0 REMARK 620 5 HOH A 635 O 85.3 86.4 169.1 89.8 REMARK 620 6 HOH A 695 O 156.6 101.3 89.0 106.4 89.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 226 OE2 REMARK 620 2 GLU B 238 OE2 81.3 REMARK 620 3 ADP B 400 O2B 161.8 93.4 REMARK 620 4 ADP B 400 O2A 107.2 82.4 89.1 REMARK 620 5 PI B 403 O2 84.7 81.3 77.3 158.1 REMARK 620 6 HOH B 659 O 94.3 170.1 93.4 90.4 107.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 238 OE1 REMARK 620 2 GLU B 238 OE2 55.1 REMARK 620 3 ADP B 400 O1B 90.2 92.9 REMARK 620 4 PI B 403 O1 152.4 99.3 102.3 REMARK 620 5 HOH B 660 O 83.1 89.8 169.5 87.3 REMARK 620 6 HOH B 661 O 100.5 155.7 87.1 104.5 86.2 REMARK 620 N 1 2 3 4 5 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 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PI A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PI B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ETH RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH MGATP DBREF 3ETJ A 1 355 UNP P09029 PURK_ECOLI 1 355 DBREF 3ETJ B 1 355 UNP P09029 PURK_ECOLI 1 355 SEQADV 3ETJ GLN A 61 UNP P09029 GLU 61 ENGINEERED MUTATION SEQADV 3ETJ ARG A 205 UNP P09029 GLN 205 ENGINEERED MUTATION SEQADV 3ETJ GLN B 61 UNP P09029 GLU 61 ENGINEERED MUTATION SEQADV 3ETJ ARG B 205 UNP P09029 GLN 205 ENGINEERED MUTATION SEQRES 1 A 355 MET LYS GLN VAL CYS VAL LEU GLY ASN GLY GLN LEU GLY SEQRES 2 A 355 ARG MET LEU ARG GLN ALA GLY GLU PRO LEU GLY ILE ALA SEQRES 3 A 355 VAL TRP PRO VAL GLY LEU ASP ALA GLU PRO ALA ALA VAL SEQRES 4 A 355 PRO PHE GLN GLN SER VAL ILE THR ALA GLU ILE GLU ARG SEQRES 5 A 355 TRP PRO GLU THR ALA LEU THR ARG GLN LEU ALA ARG HIS SEQRES 6 A 355 PRO ALA PHE VAL ASN ARG ASP VAL PHE PRO ILE ILE ALA SEQRES 7 A 355 ASP ARG LEU THR GLN LYS GLN LEU PHE ASP LYS LEU HIS SEQRES 8 A 355 LEU PRO THR ALA PRO TRP GLN LEU LEU ALA GLU ARG SER SEQRES 9 A 355 GLU TRP PRO ALA VAL PHE ASP ARG LEU GLY GLU LEU ALA SEQRES 10 A 355 ILE VAL LYS ARG ARG THR GLY GLY TYR ASP GLY ARG GLY SEQRES 11 A 355 GLN TRP ARG LEU ARG ALA ASN GLU THR GLU GLN LEU PRO SEQRES 12 A 355 ALA GLU CYS TYR GLY GLU CYS ILE VAL GLU GLN GLY ILE SEQRES 13 A 355 ASN PHE SER GLY GLU VAL SER LEU VAL GLY ALA ARG GLY SEQRES 14 A 355 PHE ASP GLY SER THR VAL PHE TYR PRO LEU THR HIS ASN SEQRES 15 A 355 LEU HIS GLN ASP GLY ILE LEU ARG THR SER VAL ALA PHE SEQRES 16 A 355 PRO GLN ALA ASN ALA GLN GLN GLN ALA ARG ALA GLU GLU SEQRES 17 A 355 MET LEU SER ALA ILE MET GLN GLU LEU GLY TYR VAL GLY SEQRES 18 A 355 VAL MET ALA MET GLU CYS PHE VAL THR PRO GLN GLY LEU SEQRES 19 A 355 LEU ILE ASN GLU LEU ALA PRO ARG VAL HIS ASN SER GLY SEQRES 20 A 355 HIS TRP THR GLN ASN GLY ALA SER ILE SER GLN PHE GLU SEQRES 21 A 355 LEU HIS LEU ARG ALA ILE THR ASP LEU PRO LEU PRO GLN SEQRES 22 A 355 PRO VAL VAL ASN ASN PRO SER VAL MET ILE ASN LEU ILE SEQRES 23 A 355 GLY SER ASP VAL ASN TYR ASP TRP LEU LYS LEU PRO LEU SEQRES 24 A 355 VAL HIS LEU HIS TRP TYR ASP LYS GLU VAL ARG PRO GLY SEQRES 25 A 355 ARG LYS VAL GLY HIS LEU ASN LEU THR ASP SER ASP THR SEQRES 26 A 355 SER ARG LEU THR ALA THR LEU GLU ALA LEU ILE PRO LEU SEQRES 27 A 355 LEU PRO PRO GLU TYR ALA SER GLY VAL ILE TRP ALA GLN SEQRES 28 A 355 SER LYS PHE GLY SEQRES 1 B 355 MET LYS GLN VAL CYS VAL LEU GLY ASN GLY GLN LEU GLY SEQRES 2 B 355 ARG MET LEU ARG GLN ALA GLY GLU PRO LEU GLY ILE ALA SEQRES 3 B 355 VAL TRP PRO VAL GLY LEU ASP ALA GLU PRO ALA ALA VAL SEQRES 4 B 355 PRO PHE GLN GLN SER VAL ILE THR ALA GLU ILE GLU ARG SEQRES 5 B 355 TRP PRO GLU THR ALA LEU THR ARG GLN LEU ALA ARG HIS SEQRES 6 B 355 PRO ALA PHE VAL ASN ARG ASP VAL PHE PRO ILE ILE ALA SEQRES 7 B 355 ASP ARG LEU THR GLN LYS GLN LEU PHE ASP LYS LEU HIS SEQRES 8 B 355 LEU PRO THR ALA PRO TRP GLN LEU LEU ALA GLU ARG SER SEQRES 9 B 355 GLU TRP PRO ALA VAL PHE ASP ARG LEU GLY GLU LEU ALA SEQRES 10 B 355 ILE VAL LYS ARG ARG THR GLY GLY TYR ASP GLY ARG GLY SEQRES 11 B 355 GLN TRP ARG LEU ARG ALA ASN GLU THR GLU GLN LEU PRO SEQRES 12 B 355 ALA GLU CYS TYR GLY GLU CYS ILE VAL GLU GLN GLY ILE SEQRES 13 B 355 ASN PHE SER GLY GLU VAL SER LEU VAL GLY ALA ARG GLY SEQRES 14 B 355 PHE ASP GLY SER THR VAL PHE TYR PRO LEU THR HIS ASN SEQRES 15 B 355 LEU HIS GLN ASP GLY ILE LEU ARG THR SER VAL ALA PHE SEQRES 16 B 355 PRO GLN ALA ASN ALA GLN GLN GLN ALA ARG ALA GLU GLU SEQRES 17 B 355 MET LEU SER ALA ILE MET GLN GLU LEU GLY TYR VAL GLY SEQRES 18 B 355 VAL MET ALA MET GLU CYS PHE VAL THR PRO GLN GLY LEU SEQRES 19 B 355 LEU ILE ASN GLU LEU ALA PRO ARG VAL HIS ASN SER GLY SEQRES 20 B 355 HIS TRP THR GLN ASN GLY ALA SER ILE SER GLN PHE GLU SEQRES 21 B 355 LEU HIS LEU ARG ALA ILE THR ASP LEU PRO LEU PRO GLN SEQRES 22 B 355 PRO VAL VAL ASN ASN PRO SER VAL MET ILE ASN LEU ILE SEQRES 23 B 355 GLY SER ASP VAL ASN TYR ASP TRP LEU LYS LEU PRO LEU SEQRES 24 B 355 VAL HIS LEU HIS TRP TYR ASP LYS GLU VAL ARG PRO GLY SEQRES 25 B 355 ARG LYS VAL GLY HIS LEU ASN LEU THR ASP SER ASP THR SEQRES 26 B 355 SER ARG LEU THR ALA THR LEU GLU ALA LEU ILE PRO LEU SEQRES 27 B 355 LEU PRO PRO GLU TYR ALA SER GLY VAL ILE TRP ALA GLN SEQRES 28 B 355 SER LYS PHE GLY HET ADP A 400 27 HET MG A 401 1 HET MG A 402 1 HET PI A 403 5 HET CL A 404 1 HET ADP B 400 27 HET MG B 401 1 HET MG B 402 1 HET PI B 403 5 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM PI HYDROGENPHOSPHATE ION HETNAM CL CHLORIDE ION FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 MG 4(MG 2+) FORMUL 6 PI 2(H O4 P 2-) FORMUL 7 CL CL 1- FORMUL 12 HOH *681(H2 O) HELIX 1 1 GLY A 10 GLU A 21 1 12 HELIX 2 2 GLU A 35 VAL A 39 5 5 HELIX 3 3 PRO A 40 SER A 44 5 5 HELIX 4 4 THR A 56 ARG A 64 1 9 HELIX 5 5 VAL A 73 ASP A 79 1 7 HELIX 6 6 ASP A 79 LEU A 90 1 12 HELIX 7 7 GLU A 102 SER A 104 5 3 HELIX 8 8 GLU A 105 GLY A 114 1 10 HELIX 9 9 ARG A 135 LEU A 142 5 8 HELIX 10 10 PRO A 143 TYR A 147 5 5 HELIX 11 11 ASN A 199 GLY A 218 1 20 HELIX 12 12 HIS A 244 HIS A 248 5 5 HELIX 13 13 TRP A 249 ALA A 254 1 6 HELIX 14 14 SER A 257 THR A 267 1 11 HELIX 15 15 ASN A 291 LEU A 297 5 7 HELIX 16 16 ASP A 324 ILE A 336 1 13 HELIX 17 17 PRO A 337 LEU A 339 5 3 HELIX 18 18 PRO A 340 GLU A 342 5 3 HELIX 19 19 TYR A 343 PHE A 354 1 12 HELIX 20 20 GLY B 10 GLU B 21 1 12 HELIX 21 21 PRO B 22 GLY B 24 5 3 HELIX 22 22 PRO B 40 SER B 44 5 5 HELIX 23 23 THR B 56 ALA B 63 1 8 HELIX 24 24 VAL B 73 ASP B 79 1 7 HELIX 25 25 ASP B 79 HIS B 91 1 13 HELIX 26 26 GLU B 102 SER B 104 5 3 HELIX 27 27 GLU B 105 GLY B 114 1 10 HELIX 28 28 GLU B 138 LEU B 142 5 5 HELIX 29 29 PRO B 143 TYR B 147 5 5 HELIX 30 30 ASN B 199 GLY B 218 1 20 HELIX 31 31 HIS B 244 HIS B 248 5 5 HELIX 32 32 TRP B 249 ALA B 254 1 6 HELIX 33 33 SER B 257 THR B 267 1 11 HELIX 34 34 ASN B 291 LEU B 297 5 7 HELIX 35 35 ASP B 324 ILE B 336 1 13 HELIX 36 36 PRO B 337 LEU B 339 5 3 HELIX 37 37 PRO B 340 GLU B 342 5 3 HELIX 38 38 TYR B 343 LYS B 353 1 11 SHEET 1 A 3 ILE A 25 VAL A 30 0 SHEET 2 A 3 LYS A 2 LEU A 7 1 N VAL A 6 O VAL A 30 SHEET 3 A 3 VAL A 45 ALA A 48 1 O THR A 47 N LEU A 7 SHEET 1 B 4 TRP A 97 LEU A 100 0 SHEET 2 B 4 CYS A 150 GLN A 154 -1 O VAL A 152 N GLN A 98 SHEET 3 B 4 ALA A 117 ARG A 121 -1 N ILE A 118 O GLU A 153 SHEET 4 B 4 GLN A 131 LEU A 134 -1 O LEU A 134 N ALA A 117 SHEET 1 C 4 THR A 174 PHE A 176 0 SHEET 2 C 4 GLY A 160 ARG A 168 -1 N ALA A 167 O VAL A 175 SHEET 3 C 4 GLY A 221 THR A 230 -1 O CYS A 227 N VAL A 162 SHEET 4 C 4 GLY A 233 ALA A 240 -1 O ASN A 237 N GLU A 226 SHEET 1 D 7 THR A 174 PHE A 176 0 SHEET 2 D 7 GLY A 160 ARG A 168 -1 N ALA A 167 O VAL A 175 SHEET 3 D 7 THR A 180 GLN A 185 -1 O THR A 180 N SER A 163 SHEET 4 D 7 ILE A 188 ALA A 194 -1 O THR A 191 N LEU A 183 SHEET 5 D 7 SER A 280 ILE A 286 -1 O ASN A 284 N ARG A 190 SHEET 6 D 7 LYS A 314 THR A 321 -1 O GLY A 316 N LEU A 285 SHEET 7 D 7 HIS A 301 TRP A 304 -1 N HIS A 301 O ASN A 319 SHEET 1 E 3 ALA B 26 VAL B 30 0 SHEET 2 E 3 GLN B 3 LEU B 7 1 N VAL B 6 O VAL B 30 SHEET 3 E 3 VAL B 45 ALA B 48 1 O THR B 47 N LEU B 7 SHEET 1 F 4 TRP B 97 LEU B 100 0 SHEET 2 F 4 CYS B 150 GLN B 154 -1 O CYS B 150 N LEU B 100 SHEET 3 F 4 ALA B 117 ARG B 121 -1 N ILE B 118 O GLU B 153 SHEET 4 F 4 GLN B 131 LEU B 134 -1 O TRP B 132 N VAL B 119 SHEET 1 G 4 THR B 174 PHE B 176 0 SHEET 2 G 4 GLY B 160 ARG B 168 -1 N ALA B 167 O VAL B 175 SHEET 3 G 4 GLY B 221 THR B 230 -1 O CYS B 227 N VAL B 162 SHEET 4 G 4 GLY B 233 ALA B 240 -1 O ASN B 237 N GLU B 226 SHEET 1 H 7 THR B 174 PHE B 176 0 SHEET 2 H 7 GLY B 160 ARG B 168 -1 N ALA B 167 O VAL B 175 SHEET 3 H 7 THR B 180 GLN B 185 -1 O THR B 180 N SER B 163 SHEET 4 H 7 ILE B 188 ALA B 194 -1 O VAL B 193 N HIS B 181 SHEET 5 H 7 SER B 280 ILE B 286 -1 O MET B 282 N SER B 192 SHEET 6 H 7 LYS B 314 THR B 321 -1 O GLY B 316 N LEU B 285 SHEET 7 H 7 HIS B 301 TRP B 304 -1 N HIS B 301 O ASN B 319 LINK OE2 GLU A 226 MG MG A 401 1555 1555 2.09 LINK OE1 GLU A 238 MG MG A 401 1555 1555 2.27 LINK OE1 GLU A 238 MG MG A 402 1555 1555 2.26 LINK OE2 GLU A 238 MG MG A 402 1555 1555 2.35 LINK O2B ADP A 400 MG MG A 401 1555 1555 2.35 LINK O2A ADP A 400 MG MG A 401 1555 1555 2.24 LINK O1B ADP A 400 MG MG A 402 1555 1555 1.91 LINK MG MG A 401 O2 PI A 403 1555 1555 2.15 LINK MG MG A 401 O HOH A 694 1555 1555 1.98 LINK MG MG A 402 O1 PI A 403 1555 1555 2.04 LINK MG MG A 402 O HOH A 635 1555 1555 2.02 LINK MG MG A 402 O HOH A 695 1555 1555 2.04 LINK OE2 GLU B 226 MG MG B 401 1555 1555 1.97 LINK OE2 GLU B 238 MG MG B 401 1555 1555 2.10 LINK OE1 GLU B 238 MG MG B 402 1555 1555 2.41 LINK OE2 GLU B 238 MG MG B 402 1555 1555 2.35 LINK O2B ADP B 400 MG MG B 401 1555 1555 2.31 LINK O2A ADP B 400 MG MG B 401 1555 1555 2.10 LINK O1B ADP B 400 MG MG B 402 1555 1555 1.93 LINK MG MG B 401 O2 PI B 403 1555 1555 2.35 LINK MG MG B 401 O HOH B 659 1555 1555 2.09 LINK MG MG B 402 O1 PI B 403 1555 1555 2.07 LINK MG MG B 402 O HOH B 660 1555 1555 2.18 LINK MG MG B 402 O HOH B 661 1555 1555 1.93 SITE 1 AC1 27 ARG A 80 LYS A 120 TYR A 126 ASP A 127 SITE 2 AC1 27 GLY A 128 GLN A 131 ARG A 133 GLU A 153 SITE 3 AC1 27 GLN A 154 GLY A 155 ILE A 156 PHE A 158 SITE 4 AC1 27 GLU A 161 HIS A 184 GLY A 187 GLU A 226 SITE 5 AC1 27 PHE A 228 ASN A 237 GLU A 238 MG A 401 SITE 6 AC1 27 MG A 402 PI A 403 HOH A 463 HOH A 688 SITE 7 AC1 27 HOH A 693 HOH A 694 HOH A 695 SITE 1 AC2 5 GLU A 226 GLU A 238 ADP A 400 PI A 403 SITE 2 AC2 5 HOH A 694 SITE 1 AC3 5 GLU A 238 ADP A 400 PI A 403 HOH A 635 SITE 2 AC3 5 HOH A 695 SITE 1 AC4 14 TYR A 126 ASP A 127 GLU A 226 GLU A 238 SITE 2 AC4 14 ARG A 242 HIS A 244 ADP A 400 MG A 401 SITE 3 AC4 14 MG A 402 HOH A 473 HOH A 625 HOH A 635 SITE 4 AC4 14 HOH A 694 HOH A 696 SITE 1 AC5 23 ARG B 80 ILE B 118 LYS B 120 GLN B 131 SITE 2 AC5 23 GLU B 153 GLN B 154 GLY B 155 ILE B 156 SITE 3 AC5 23 PHE B 158 GLU B 161 HIS B 184 GLU B 226 SITE 4 AC5 23 PHE B 228 ASN B 237 GLU B 238 MG B 401 SITE 5 AC5 23 MG B 402 PI B 403 HOH B 497 HOH B 530 SITE 6 AC5 23 HOH B 659 HOH B 661 HOH B 666 SITE 1 AC6 5 GLU B 226 GLU B 238 ADP B 400 PI B 403 SITE 2 AC6 5 HOH B 659 SITE 1 AC7 5 GLU B 238 ADP B 400 PI B 403 HOH B 660 SITE 2 AC7 5 HOH B 661 SITE 1 AC8 10 GLU B 226 GLU B 238 ARG B 242 HIS B 244 SITE 2 AC8 10 ADP B 400 MG B 401 MG B 402 HOH B 442 SITE 3 AC8 10 HOH B 660 HOH B 664 SITE 1 AC9 3 ARG A 242 VAL A 243 HIS A 262 CRYST1 128.800 70.500 88.700 90.00 124.30 90.00 C 1 2 1 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 0.007764 0.000000 0.005296 0.00000 SCALE2 0.000000 0.014184 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013647 0.00000