PDB Short entry for 1KBL HEADER TRANSFERASE 06-NOV-01 1KBL TITLE PYRUVATE PHOSPHATE DIKINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRUVATE PHOSPHATE DIKINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPDK; COMPND 5 EC: 2.7.9.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM SYMBIOSUM; SOURCE 3 ORGANISM_TAXID: 1512; SOURCE 4 GENE: PPDK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM 101; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PACYC184-D12; SOURCE 10 EXPRESSION_SYSTEM_GENE: PPDK KEYWDS TRANSFERASE, PHOSPHOTRANSFERASE, KINASE EXPDTA X-RAY DIFFRACTION AUTHOR O.HERZBERG,C.C.CHEN,S.LIU REVDAT 5 16-AUG-23 1KBL 1 REMARK REVDAT 4 13-JUL-11 1KBL 1 VERSN REVDAT 3 24-FEB-09 1KBL 1 VERSN REVDAT 2 12-OCT-04 1KBL 1 SCALE1 SCALE2 SCALE3 REVDAT 1 30-JAN-02 1KBL 0 JRNL AUTH O.HERZBERG,C.C.CHEN,S.LIU,A.TEMPCZYK,A.HOWARD,M.WEI,D.YE, JRNL AUTH 2 D.DUNAWAY-MARIANO JRNL TITL PYRUVATE SITE OF PYRUVATE PHOSPHATE DIKINASE: CRYSTAL JRNL TITL 2 STRUCTURE OF THE ENZYME-PHOSPHONOPYRUVATE COMPLEX, AND JRNL TITL 3 MUTANT ANALYSIS JRNL REF BIOCHEMISTRY V. 41 780 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 11790099 JRNL DOI 10.1021/BI011799+ REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.HERZBERG,C.C.CHEN,G.KAPADIA,M.MCGUIRE,L.J.CARROLL,S.J.NOH, REMARK 1 AUTH 2 D.DUNAWAY-MARIANO REMARK 1 TITL SWIVELING-DOMAIN MECHANISM FOR ENZYMATIC PHOSPHOTRANSFER REMARK 1 TITL 2 BETWEEN REMOTE REACTION SITES REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 93 2652 1996 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.93.7.2652 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.MCGUIRE,K.HUANG,G.KAPADIA,O.HERZBERG,D.DUNAWAY-MARIANO REMARK 1 TITL LOCATION OF THE PHOSPHATE BINDING SITE WITHIN CLOSTRIDIUM REMARK 1 TITL 2 SYMBIOSUM PYRUVATE PHOSPHATE DIKINASE REMARK 1 REF BIOCHEMISTRY V. 37 13463 1998 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI980920I REMARK 1 REFERENCE 3 REMARK 1 AUTH M.WEI,Z.LI,D.YE,O.HERZBERG,D.DUNAWAY-MARIANO REMARK 1 TITL IDENTIFICATION OF DOMAIN-DOMAIN DOCKING SITES WITHIN REMARK 1 TITL 2 CLOSTRIDIUM SYMBIOSUM PYRUVATE PHOSPHATE DIKINASE BY AMINO REMARK 1 TITL 3 ACID REPLACEMENT REMARK 1 REF J.BIOL.CHEM. V. 275 41156 2000 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M006149200 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.200 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 72384 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) : 0.195 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500 REMARK 3 FREE R VALUE TEST SET COUNT : 4390 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6752 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 879 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.021 REMARK 3 BOND ANGLES (DEGREES) : 1.910 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KBL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014781. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-95 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3 REMARK 200 MONOCHROMATOR : TOROIDAL MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79262 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : 0.05100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.40500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PPDK + PHOSPHONOPYRUVATE (PDB ENTRY 1KC7) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50-54% SATURATED AMMONIUM SULFATE, 10 REMARK 280 MG/ML PROTEIN SOLUTION IN 100MM KCL AND 20MM IMIDAZOLE BUFFER REMARK 280 (PH 6.5), 100 MM HEPES BUFFER (PH 7.0), VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 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 300 REMARK: A DIMER GENERATED BY A CRYSTALLOGRAPHIC REMARK 300 2-FOLD AXIS: REMARK 300 -1.0 0.0 0.0 89.837 REMARK 300 0.0 1.0 0.0 0.0 REMARK 300 0.0 0.0 -1.0 0.0 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: 4060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 67630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -146.0 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 BIOMT1 2 -1.000000 0.000000 0.000000 89.83700 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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: 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 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 S SO4 A 904 LIES ON A SPECIAL POSITION. REMARK 375 O3 SO4 A 904 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 LYS A 874 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 79 CD CE NZ REMARK 480 LYS A 154 CB CG CD CE NZ REMARK 480 LYS A 182 CE NZ REMARK 480 LYS A 371 CD CE NZ REMARK 480 LYS A 387 CB CG CD CE NZ REMARK 480 GLU A 478 CD OE1 OE2 REMARK 480 GLU A 585 CG CD OE1 OE2 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 O ALA A 646 O HOH A 1656 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 773 SD MET A 773 CE 0.352 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 537 NE - CZ - NH1 ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 537 NE - CZ - NH2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ARG A 576 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 617 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 617 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 858 NE - CZ - NH1 ANGL. DEV. = 3.0 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 LYS A 55 66.21 33.79 REMARK 500 MET A 145 -160.55 -103.96 REMARK 500 GLU A 146 48.59 -141.12 REMARK 500 GLU A 189 13.10 -62.16 REMARK 500 MET A 191 32.81 -95.59 REMARK 500 ASN A 275 71.03 54.73 REMARK 500 ALA A 395 -149.99 -161.48 REMARK 500 GLU A 478 -70.03 -48.58 REMARK 500 SER A 516 -135.15 -115.60 REMARK 500 SER A 518 -172.32 -62.67 REMARK 500 ASP A 582 16.16 -140.10 REMARK 500 PHE A 785 -19.72 -159.14 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 NH4 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 906 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DIK RELATED DB: PDB REMARK 900 1DIK IS PYRUVATE PHOSPHATE DIKINASE (ROOM TEMPERATURE DATA). DBREF 1KBL A 2 874 UNP P22983 PPDK_CLOSY 1 873 SEQRES 1 A 873 ALA LYS TRP VAL TYR LYS PHE GLU GLU GLY ASN ALA SER SEQRES 2 A 873 MET ARG ASN LEU LEU GLY GLY LYS GLY CYS ASN LEU ALA SEQRES 3 A 873 GLU MET THR ILE LEU GLY MET PRO ILE PRO GLN GLY PHE SEQRES 4 A 873 THR VAL THR THR GLU ALA CYS THR GLU TYR TYR ASN SER SEQRES 5 A 873 GLY LYS GLN ILE THR GLN GLU ILE GLN ASP GLN ILE PHE SEQRES 6 A 873 GLU ALA ILE THR TRP LEU GLU GLU LEU ASN GLY LYS LYS SEQRES 7 A 873 PHE GLY ASP THR GLU ASP PRO LEU LEU VAL SER VAL ARG SEQRES 8 A 873 SER GLY ALA ARG ALA SER MET PRO GLY MET MET ASP THR SEQRES 9 A 873 ILE LEU ASN LEU GLY LEU ASN ASP VAL ALA VAL GLU GLY SEQRES 10 A 873 PHE ALA LYS LYS THR GLY ASN PRO ARG PHE ALA TYR ASP SEQRES 11 A 873 SER TYR ARG ARG PHE ILE GLN MET TYR SER ASP VAL VAL SEQRES 12 A 873 MET GLU VAL PRO LYS SER HIS PHE GLU LYS ILE ILE ASP SEQRES 13 A 873 ALA MET LYS GLU GLU LYS GLY VAL HIS PHE ASP THR ASP SEQRES 14 A 873 LEU THR ALA ASP ASP LEU LYS GLU LEU ALA GLU LYS PHE SEQRES 15 A 873 LYS ALA VAL TYR LYS GLU ALA MET ASN GLY GLU GLU PHE SEQRES 16 A 873 PRO GLN GLU PRO LYS ASP GLN LEU MET GLY ALA VAL LYS SEQRES 17 A 873 ALA VAL PHE ARG SER TRP ASP ASN PRO ARG ALA ILE VAL SEQRES 18 A 873 TYR ARG ARG MET ASN ASP ILE PRO GLY ASP TRP GLY THR SEQRES 19 A 873 ALA VAL ASN VAL GLN THR MET VAL PHE GLY ASN LYS GLY SEQRES 20 A 873 GLU THR SER GLY THR GLY VAL ALA PHE THR ARG ASN PRO SEQRES 21 A 873 SER THR GLY GLU LYS GLY ILE TYR GLY GLU TYR LEU ILE SEQRES 22 A 873 ASN ALA GLN GLY GLU ASP VAL VAL ALA GLY VAL ARG THR SEQRES 23 A 873 PRO GLN PRO ILE THR GLN LEU GLU ASN ASP MET PRO ASP SEQRES 24 A 873 CYS TYR LYS GLN PHE MET ASP LEU ALA MET LYS LEU GLU SEQRES 25 A 873 LYS HIS PHE ARG ASP MET GLN ASP MET GLU PHE THR ILE SEQRES 26 A 873 GLU GLU GLY LYS LEU TYR PHE LEU GLN THR ARG ASN GLY SEQRES 27 A 873 LYS ARG THR ALA PRO ALA ALA LEU GLN ILE ALA CYS ASP SEQRES 28 A 873 LEU VAL ASP GLU GLY MET ILE THR GLU GLU GLU ALA VAL SEQRES 29 A 873 VAL ARG ILE GLU ALA LYS SER LEU ASP GLN LEU LEU HIS SEQRES 30 A 873 PRO THR PHE ASN PRO ALA ALA LEU LYS ALA GLY GLU VAL SEQRES 31 A 873 ILE GLY SER ALA LEU PRO ALA SER PRO GLY ALA ALA ALA SEQRES 32 A 873 GLY LYS VAL TYR PHE THR ALA ASP GLU ALA LYS ALA ALA SEQRES 33 A 873 HIS GLU LYS GLY GLU ARG VAL ILE LEU VAL ARG LEU GLU SEQRES 34 A 873 THR SER PRO GLU ASP ILE GLU GLY MET HIS ALA ALA GLU SEQRES 35 A 873 GLY ILE LEU THR VAL ARG GLY GLY MET THR SER HIS ALA SEQRES 36 A 873 ALA VAL VAL ALA ARG GLY MET GLY THR CYS CYS VAL SER SEQRES 37 A 873 GLY CYS GLY GLU ILE LYS ILE ASN GLU GLU ALA LYS THR SEQRES 38 A 873 PHE GLU LEU GLY GLY HIS THR PHE ALA GLU GLY ASP TYR SEQRES 39 A 873 ILE SER LEU ASP GLY SER THR GLY LYS ILE TYR LYS GLY SEQRES 40 A 873 ASP ILE GLU THR GLN GLU ALA SER VAL SER GLY SER PHE SEQRES 41 A 873 GLU ARG ILE MET VAL TRP ALA ASP LYS PHE ARG THR LEU SEQRES 42 A 873 LYS VAL ARG THR ASN ALA ASP THR PRO GLU ASP THR LEU SEQRES 43 A 873 ASN ALA VAL LYS LEU GLY ALA GLU GLY ILE GLY LEU CYS SEQRES 44 A 873 ARG THR GLU HIS MET PHE PHE GLU ALA ASP ARG ILE MET SEQRES 45 A 873 LYS ILE ARG LYS MET ILE LEU SER ASP SER VAL GLU ALA SEQRES 46 A 873 ARG GLU GLU ALA LEU ASN GLU LEU ILE PRO PHE GLN LYS SEQRES 47 A 873 GLY ASP PHE LYS ALA MET TYR LYS ALA LEU GLU GLY ARG SEQRES 48 A 873 PRO MET THR VAL ARG TYR LEU ASP PRO PRO LEU HIS GLU SEQRES 49 A 873 PHE VAL PRO HIS THR GLU GLU GLU GLN ALA GLU LEU ALA SEQRES 50 A 873 LYS ASN MET GLY LEU THR LEU ALA GLU VAL LYS ALA LYS SEQRES 51 A 873 VAL ASP GLU LEU HIS GLU PHE ASN PRO MET MET GLY HIS SEQRES 52 A 873 ARG GLY CYS ARG LEU ALA VAL THR TYR PRO GLU ILE ALA SEQRES 53 A 873 LYS MET GLN THR ARG ALA VAL MET GLU ALA ALA ILE GLU SEQRES 54 A 873 VAL LYS GLU GLU THR GLY ILE ASP ILE VAL PRO GLU ILE SEQRES 55 A 873 MET ILE PRO LEU VAL GLY GLU LYS LYS GLU LEU LYS PHE SEQRES 56 A 873 VAL LYS ASP VAL VAL VAL GLU VAL ALA GLU GLN VAL LYS SEQRES 57 A 873 LYS GLU LYS GLY SER ASP MET GLN TYR HIS ILE GLY THR SEQRES 58 A 873 MET ILE GLU ILE PRO ARG ALA ALA LEU THR ALA ASP ALA SEQRES 59 A 873 ILE ALA GLU GLU ALA GLU PHE PHE SER PHE GLY THR ASN SEQRES 60 A 873 ASP LEU THR GLN MET THR PHE GLY PHE SER ARG ASP ASP SEQRES 61 A 873 ALA GLY LYS PHE LEU ASP SER TYR TYR LYS ALA LYS ILE SEQRES 62 A 873 TYR GLU SER ASP PRO PHE ALA ARG LEU ASP GLN THR GLY SEQRES 63 A 873 VAL GLY GLN LEU VAL GLU MET ALA VAL LYS LYS GLY ARG SEQRES 64 A 873 GLN THR ARG PRO GLY LEU LYS CYS GLY ILE CYS GLY GLU SEQRES 65 A 873 HIS GLY GLY ASP PRO SER SER VAL GLU PHE CYS HIS LYS SEQRES 66 A 873 VAL GLY LEU ASN TYR VAL SER CYS SER PRO PHE ARG VAL SEQRES 67 A 873 PRO ILE ALA ARG LEU ALA ALA ALA GLN ALA ALA LEU ASN SEQRES 68 A 873 ASN LYS HET NH4 A 901 1 HET SO4 A 902 5 HET SO4 A 903 5 HET SO4 A 904 5 HET SO4 A 905 5 HET SO4 A 906 5 HETNAM NH4 AMMONIUM ION HETNAM SO4 SULFATE ION FORMUL 2 NH4 H4 N 1+ FORMUL 3 SO4 5(O4 S 2-) FORMUL 8 HOH *879(H2 O) HELIX 1 1 GLU A 9 GLY A 11 5 3 HELIX 2 2 ASN A 12 SER A 14 5 3 HELIX 3 3 MET A 15 LEU A 32 1 18 HELIX 4 4 THR A 43 ASN A 52 1 10 HELIX 5 5 THR A 58 GLY A 77 1 20 HELIX 6 6 VAL A 114 GLY A 124 1 11 HELIX 7 7 ASN A 125 MET A 145 1 21 HELIX 8 8 PRO A 148 LYS A 163 1 16 HELIX 9 9 PHE A 167 LEU A 171 5 5 HELIX 10 10 THR A 172 GLU A 189 1 18 HELIX 11 11 GLU A 199 TRP A 215 1 17 HELIX 12 12 ASN A 217 ASN A 227 1 11 HELIX 13 13 PRO A 230 GLY A 234 5 5 HELIX 14 14 GLN A 277 GLY A 284 1 8 HELIX 15 15 GLN A 293 MET A 298 1 6 HELIX 16 16 MET A 298 ARG A 317 1 20 HELIX 17 17 THR A 342 GLU A 356 1 15 HELIX 18 18 THR A 360 ILE A 368 1 9 HELIX 19 19 GLU A 369 HIS A 378 5 10 HELIX 20 20 ASN A 382 GLY A 389 1 8 HELIX 21 21 THR A 410 LYS A 420 1 11 HELIX 22 22 SER A 432 GLU A 434 5 3 HELIX 23 23 ASP A 435 ALA A 442 1 8 HELIX 24 24 SER A 454 GLY A 464 1 11 HELIX 25 25 SER A 518 ARG A 532 1 15 HELIX 26 26 THR A 542 LEU A 552 1 11 HELIX 27 27 GLU A 563 GLU A 568 1 6 HELIX 28 28 GLU A 568 SER A 581 1 14 HELIX 29 29 SER A 583 GLU A 593 1 11 HELIX 30 30 LEU A 594 GLU A 610 1 17 HELIX 31 31 PRO A 622 VAL A 627 5 6 HELIX 32 32 THR A 630 GLY A 642 1 13 HELIX 33 33 THR A 644 HIS A 656 1 13 HELIX 34 34 ASN A 659 GLY A 663 5 5 HELIX 35 35 GLY A 666 TYR A 673 1 8 HELIX 36 36 TYR A 673 GLY A 696 1 24 HELIX 37 37 GLU A 710 GLY A 733 1 24 HELIX 38 38 ILE A 746 THR A 752 1 7 HELIX 39 39 THR A 752 ALA A 757 1 6 HELIX 40 40 GLY A 766 GLY A 776 1 11 HELIX 41 41 SER A 778 ALA A 792 1 15 HELIX 42 42 GLY A 807 ARG A 823 1 17 HELIX 43 43 GLY A 832 GLY A 836 5 5 HELIX 44 44 ASP A 837 VAL A 847 1 11 HELIX 45 45 SER A 855 PHE A 857 5 3 HELIX 46 46 ARG A 858 ASN A 873 1 16 SHEET 1 A 5 VAL A 5 LYS A 7 0 SHEET 2 A 5 GLY A 39 VAL A 42 -1 O THR A 41 N TYR A 6 SHEET 3 A 5 ALA A 236 THR A 241 -1 O VAL A 239 N PHE A 40 SHEET 4 A 5 VAL A 89 GLY A 94 -1 N ARG A 92 O ASN A 238 SHEET 5 A 5 THR A 105 LEU A 109 -1 O ILE A 106 N VAL A 91 SHEET 1 B 5 GLN A 289 PRO A 290 0 SHEET 2 B 5 LYS A 266 ILE A 274 -1 N TYR A 272 O GLN A 289 SHEET 3 B 5 GLY A 252 ARG A 259 -1 N PHE A 257 O TYR A 269 SHEET 4 B 5 GLN A 320 GLU A 327 -1 O ILE A 326 N GLY A 252 SHEET 5 B 5 LYS A 330 ASN A 338 -1 O TYR A 332 N THR A 325 SHEET 1 C 2 THR A 380 PHE A 381 0 SHEET 2 C 2 THR A 512 GLN A 513 -1 O GLN A 513 N THR A 380 SHEET 1 D 8 VAL A 391 SER A 394 0 SHEET 2 D 8 LYS A 504 LYS A 507 -1 O ILE A 505 N GLY A 393 SHEET 3 D 8 TYR A 495 ASP A 499 -1 N SER A 497 O TYR A 506 SHEET 4 D 8 ALA A 402 TYR A 408 -1 N ALA A 403 O LEU A 498 SHEET 5 D 8 VAL A 424 ARG A 428 1 O ILE A 425 N LYS A 406 SHEET 6 D 8 GLY A 444 THR A 447 1 O LEU A 446 N LEU A 426 SHEET 7 D 8 CYS A 466 SER A 469 1 O VAL A 468 N ILE A 445 SHEET 8 D 8 LEU A 396 SER A 399 -1 N SER A 399 O CYS A 467 SHEET 1 E 3 LYS A 475 ASN A 477 0 SHEET 2 E 3 THR A 482 LEU A 485 -1 O THR A 482 N ASN A 477 SHEET 3 E 3 HIS A 488 ALA A 491 -1 O PHE A 490 N PHE A 483 SHEET 1 F 8 LYS A 827 ILE A 830 0 SHEET 2 F 8 PHE A 762 PHE A 765 1 N PHE A 765 O GLY A 829 SHEET 3 F 8 HIS A 739 ILE A 744 1 N ILE A 744 O SER A 764 SHEET 4 F 8 GLU A 702 ILE A 705 1 N ILE A 703 O GLY A 741 SHEET 5 F 8 MET A 614 ARG A 617 1 N VAL A 616 O GLU A 702 SHEET 6 F 8 ILE A 557 CYS A 560 1 N ILE A 557 O THR A 615 SHEET 7 F 8 LYS A 535 ASN A 539 1 N THR A 538 O GLY A 558 SHEET 8 F 8 TYR A 851 CYS A 854 1 O VAL A 852 N ARG A 537 SITE 1 AC1 6 ASP A 620 GLU A 745 ASP A 769 SO4 A 905 SITE 2 AC1 6 HOH A1048 HOH A1511 SITE 1 AC2 12 LYS A 22 MET A 99 PRO A 100 GLY A 101 SITE 2 AC2 12 MET A 102 MET A 103 ARG A 337 HOH A 916 SITE 3 AC2 12 HOH A 949 HOH A 966 HOH A1436 HOH A1769 SITE 1 AC3 5 LYS A 718 GLU A 758 ARG A 823 HOH A1405 SITE 2 AC3 5 HOH A1476 SITE 1 AC4 4 ARG A 523 TRP A 527 HOH A1007 HOH A1208 SITE 1 AC5 7 ARG A 617 ASN A 768 NH4 A 901 HOH A 952 SITE 2 AC5 7 HOH A1075 HOH A1250 HOH A1511 SITE 1 AC6 6 PRO A 660 MET A 661 ARG A 665 HOH A1112 SITE 2 AC6 6 HOH A1168 HOH A1205 CRYST1 89.837 58.838 102.949 90.00 94.84 90.00 P 1 2 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 0.011131 0.000000 0.000942 0.00000 SCALE2 0.000000 0.016996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009748 0.00000