PDB Short entry for 1VBG HEADER TRANSFERASE 26-FEB-04 1VBG TITLE PYRUVATE PHOSPHATE DIKINASE FROM MAIZE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRUVATE,ORTHOPHOSPHATE DIKINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYRUVATE PHOSPHATE DIKINASE; COMPND 5 EC: 2.7.9.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 3 ORGANISM_TAXID: 4577; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PKK233-2 KEYWDS TRANSFERASE, MAIZE, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, KEYWDS 2 RSGI, STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKANISHI,T.NAKATSU,M.MATSUOKA,K.SAKATA,H.KATO,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 5 25-OCT-23 1VBG 1 REMARK LINK REVDAT 4 04-OCT-17 1VBG 1 REMARK REVDAT 3 13-JUL-11 1VBG 1 VERSN REVDAT 2 24-FEB-09 1VBG 1 VERSN REVDAT 1 08-MAR-05 1VBG 0 JRNL AUTH T.NAKANISHI,T.NAKATSU,M.MATSUOKA,K.SAKATA,H.KATO JRNL TITL CRYSTAL STRUCTURES OF PYRUVATE PHOSPHATE DIKINASE FROM MAIZE JRNL TITL 2 REVEALED AN ALTERNATIVE CONFORMATION IN THE SWIVELING-DOMAIN JRNL TITL 3 MOTION JRNL REF BIOCHEMISTRY V. 44 1136 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15667207 JRNL DOI 10.1021/BI0484522 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.NAKANISHI,Y.OHKI,J.ODA,M.MATSUOKA,K.SAKATA,H.KATO REMARK 1 TITL PURIFICATION, CRYSTALLIZATION AND PRELIMINARY X-RAY REMARK 1 TITL 2 DIFFRACTION STUDIES ON PYRUVATE PHOSPHATE DIKINASE FROM REMARK 1 TITL 3 MAIZE REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 60 193 2004 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 14684927 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.MATSUOKA,Y.OZEKI,N.YAMAMOTO,H.HIRANO,Y.KANO-MURAKAMI, REMARK 1 AUTH 2 Y.TANAKA REMARK 1 TITL PRIMARY STRUCTURE OF MAIZE PYRUVATE, ORTHOPHOSPHATE DIKINASE REMARK 1 TITL 2 AS DEDUCED FROM CDNA SEQUENCE REMARK 1 REF J.BIOL.CHEM. V. 263 11080 1988 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 2841317 REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2321429.500 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 50976 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) : 0.209 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2545 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 8032 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 409 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6551 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 248 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.65000 REMARK 3 B22 (A**2) : -2.17000 REMARK 3 B33 (A**2) : -0.48000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 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) : 22.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.880 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) : 2.300 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.240 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.940 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.240 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 41.51 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VBG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000006429. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51096 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 73.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.650 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30100 REMARK 200 R SYM FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1DIK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, MAGNESIUM SULFATE, GLYCEROL, REMARK 280 PH 6.5, VAPOR 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 54.07850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.11100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.07850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 50.11100 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 70490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -127.0 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 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 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 THR A 1 REMARK 465 THR A 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 15 CG CD OE1 OE2 REMARK 470 LYS A 21 CG CD CE NZ REMARK 470 GLU A 22 CD OE1 OE2 REMARK 470 GLU A 50 CG CD OE1 OE2 REMARK 470 GLN A 53 CG CD OE1 NE2 REMARK 470 GLN A 75 CG CD OE1 NE2 REMARK 470 GLU A 79 CG CD OE1 OE2 REMARK 470 ARG A 90 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 109 CG OD1 OD2 REMARK 470 GLU A 130 CG CD OE1 OE2 REMARK 470 GLU A 161 CG CD OE1 OE2 REMARK 470 HIS A 162 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 164 CB CG CD CE NZ REMARK 470 GLU A 165 CG CD OE1 OE2 REMARK 470 LYS A 167 CG CD CE NZ REMARK 470 LEU A 169 CG CD1 CD2 REMARK 470 LYS A 170 CG CD CE NZ REMARK 470 ASN A 171 CG OD1 ND2 REMARK 470 GLN A 231 CG CD OE1 NE2 REMARK 470 THR A 233 OG1 CG2 REMARK 470 LEU A 300 CG CD1 CD2 REMARK 470 GLN A 303 CG CD OE1 NE2 REMARK 470 LYS A 391 CG CD CE NZ REMARK 470 GLU A 451 CG CD OE1 OE2 REMARK 470 ASP A 481 CG OD1 OD2 REMARK 470 ASN A 635 CG OD1 ND2 REMARK 470 GLN A 651 CG CD OE1 NE2 REMARK 470 GLU A 652 CG CD OE1 OE2 REMARK 470 LYS A 660 CD CE NZ REMARK 470 GLN A 801 CD OE1 NE2 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 97 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 535 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 863 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 868 NE - CZ - NH2 ANGL. DEV. = 3.4 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 LYS A 11 103.29 -56.54 REMARK 500 MET A 20 53.67 -93.16 REMARK 500 SER A 48 157.64 -43.04 REMARK 500 ALA A 58 26.61 -75.86 REMARK 500 ASP A 172 -29.98 -27.55 REMARK 500 THR A 173 -4.13 -57.46 REMARK 500 ASN A 230 52.41 -166.92 REMARK 500 GLN A 231 111.59 -2.72 REMARK 500 LEU A 235 -63.46 -8.33 REMARK 500 ARG A 236 -1.63 88.65 REMARK 500 MET A 250 49.58 -97.57 REMARK 500 ASN A 252 30.55 -84.65 REMARK 500 ASN A 278 70.55 40.83 REMARK 500 ALA A 279 174.83 175.09 REMARK 500 GLU A 292 -163.97 -101.86 REMARK 500 ASN A 332 -7.28 71.45 REMARK 500 LEU A 337 -97.98 -96.22 REMARK 500 GLU A 385 -86.70 -59.90 REMARK 500 SER A 402 115.04 -161.64 REMARK 500 PRO A 436 -7.90 -55.63 REMARK 500 ASP A 614 111.96 -33.70 REMARK 500 LEU A 623 118.11 -38.01 REMARK 500 GLU A 750 -8.99 -142.08 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 SER A 783 12.56 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 A2000 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 750 OE1 REMARK 620 2 ASP A 774 OD2 84.5 REMARK 620 3 HOH A3003 O 87.5 85.8 REMARK 620 4 HOH A3008 O 84.4 90.6 171.4 REMARK 620 5 HOH A3017 O 177.1 95.7 95.4 92.8 REMARK 620 6 HOH A3020 O 84.3 167.8 89.0 93.0 95.7 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 MG A 2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 3000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 3002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VBH RELATED DB: PDB REMARK 900 PYRUVATE PHOSPHATE DIKINASE WITH BOUND MG-PEP REMARK 900 RELATED ID: MY_001000036.1 RELATED DB: TARGETDB DBREF 1VBG A 1 876 UNP P11155 PPDK_MAIZE 72 947 SEQADV 1VBG PHE A 819 UNP P11155 LEU 890 SEE REMARK 999 SEQRES 1 A 876 THR THR LYS LYS ARG VAL PHE HIS PHE GLY LYS GLY LYS SEQRES 2 A 876 SER GLU GLY ASN LYS THR MET LYS GLU LEU LEU GLY GLY SEQRES 3 A 876 LYS GLY ALA ASN LEU ALA GLU MET ALA SER ILE GLY LEU SEQRES 4 A 876 SER VAL PRO PRO GLY PHE THR VAL SER THR GLU ALA CYS SEQRES 5 A 876 GLN GLN TYR GLN ASP ALA GLY CYS ALA LEU PRO ALA GLY SEQRES 6 A 876 LEU TRP ALA GLU ILE VAL ASP GLY LEU GLN TRP VAL GLU SEQRES 7 A 876 GLU TYR MET GLY ALA THR LEU GLY ASP PRO GLN ARG PRO SEQRES 8 A 876 LEU LEU LEU SER VAL ARG SER GLY ALA ALA VAL SER MET SEQRES 9 A 876 PRO GLY MET MET ASP THR VAL LEU ASN LEU GLY LEU ASN SEQRES 10 A 876 ASP GLU VAL ALA ALA GLY LEU ALA ALA LYS SER GLY GLU SEQRES 11 A 876 ARG PHE ALA TYR ASP SER PHE ARG ARG PHE LEU ASP MET SEQRES 12 A 876 PHE GLY ASN VAL VAL MET ASP ILE PRO ARG SER LEU PHE SEQRES 13 A 876 GLU GLU LYS LEU GLU HIS MET LYS GLU SER LYS GLY LEU SEQRES 14 A 876 LYS ASN ASP THR ASP LEU THR ALA SER ASP LEU LYS GLU SEQRES 15 A 876 LEU VAL GLY GLN TYR LYS GLU VAL TYR LEU SER ALA LYS SEQRES 16 A 876 GLY GLU PRO PHE PRO SER ASP PRO LYS LYS GLN LEU GLU SEQRES 17 A 876 LEU ALA VAL LEU ALA VAL PHE ASN SER TRP GLU SER PRO SEQRES 18 A 876 ARG ALA LYS LYS TYR ARG SER ILE ASN GLN ILE THR GLY SEQRES 19 A 876 LEU ARG GLY THR ALA VAL ASN VAL GLN CYS MET VAL PHE SEQRES 20 A 876 GLY ASN MET GLY ASN THR SER GLY THR GLY VAL LEU PHE SEQRES 21 A 876 THR ARG ASN PRO ASN THR GLY GLU LYS LYS LEU TYR GLY SEQRES 22 A 876 GLU PHE LEU VAL ASN ALA GLN GLY GLU ASP VAL VAL ALA SEQRES 23 A 876 GLY ILE ARG THR PRO GLU ASP LEU ASP ALA MET LYS ASN SEQRES 24 A 876 LEU MET PRO GLN ALA TYR ASP GLU LEU VAL GLU ASN CYS SEQRES 25 A 876 ASN ILE LEU GLU SER HIS TYR LYS GLU MET GLN ASP ILE SEQRES 26 A 876 GLU PHE THR VAL GLN GLU ASN ARG LEU TRP MET LEU GLN SEQRES 27 A 876 CYS ARG THR GLY LYS ARG THR GLY LYS SER ALA VAL LYS SEQRES 28 A 876 ILE ALA VAL ASP MET VAL ASN GLU GLY LEU VAL GLU PRO SEQRES 29 A 876 ARG SER ALA ILE LYS MET VAL GLU PRO GLY HIS LEU ASP SEQRES 30 A 876 GLN LEU LEU HIS PRO GLN PHE GLU ASN PRO SER ALA TYR SEQRES 31 A 876 LYS ASP GLN VAL ILE ALA THR GLY LEU PRO ALA SER PRO SEQRES 32 A 876 GLY ALA ALA VAL GLY GLN VAL VAL PHE THR ALA GLU ASP SEQRES 33 A 876 ALA GLU ALA TRP HIS SER GLN GLY LYS ALA ALA ILE LEU SEQRES 34 A 876 VAL ARG ALA GLU THR SER PRO GLU ASP VAL GLY GLY MET SEQRES 35 A 876 HIS ALA ALA VAL GLY ILE LEU THR GLU ARG GLY GLY MET SEQRES 36 A 876 THR SER HIS ALA ALA VAL VAL ALA ARG GLY TRP GLY LYS SEQRES 37 A 876 CYS CYS VAL SER GLY CYS SER GLY ILE ARG VAL ASN ASP SEQRES 38 A 876 ALA GLU LYS LEU VAL THR ILE GLY GLY HIS VAL LEU ARG SEQRES 39 A 876 GLU GLY GLU TRP LEU SER LEU ASN GLY SER THR GLY GLU SEQRES 40 A 876 VAL ILE LEU GLY LYS GLN PRO LEU SER PRO PRO ALA LEU SEQRES 41 A 876 SER GLY ASP LEU GLY THR PHE MET ALA TRP VAL ASP ASP SEQRES 42 A 876 VAL ARG LYS LEU LYS VAL LEU ALA ASN ALA ASP THR PRO SEQRES 43 A 876 ASP ASP ALA LEU THR ALA ARG ASN ASN GLY ALA GLN GLY SEQRES 44 A 876 ILE GLY LEU CYS ARG THR GLU HIS MET PHE PHE ALA SER SEQRES 45 A 876 ASP GLU ARG ILE LYS ALA VAL ARG GLN MET ILE MET ALA SEQRES 46 A 876 PRO THR LEU GLU LEU ARG GLN GLN ALA LEU ASP ARG LEU SEQRES 47 A 876 LEU PRO TYR GLN ARG SER ASP PHE GLU GLY ILE PHE ARG SEQRES 48 A 876 ALA MET ASP GLY LEU PRO VAL THR ILE ARG LEU LEU ASP SEQRES 49 A 876 PRO PRO LEU HIS GLU PHE LEU PRO GLU GLY ASN ILE GLU SEQRES 50 A 876 ASP ILE VAL SER GLU LEU CYS ALA GLU THR GLY ALA ASN SEQRES 51 A 876 GLN GLU ASP ALA LEU ALA ARG ILE GLU LYS LEU SER GLU SEQRES 52 A 876 VAL ASN PRO MET LEU GLY PHE ARG GLY CYS ARG LEU GLY SEQRES 53 A 876 ILE SER TYR PRO GLU LEU THR GLU MET GLN ALA ARG ALA SEQRES 54 A 876 ILE PHE GLU ALA ALA ILE ALA MET THR ASN GLN GLY VAL SEQRES 55 A 876 GLN VAL PHE PRO GLU ILE MET VAL PRO LEU VAL GLY THR SEQRES 56 A 876 PRO GLN GLU LEU GLY HIS GLN VAL THR LEU ILE ARG GLN SEQRES 57 A 876 VAL ALA GLU LYS VAL PHE ALA ASN VAL GLY LYS THR ILE SEQRES 58 A 876 GLY TYR LYS VAL GLY THR MET ILE GLU ILE PRO ARG ALA SEQRES 59 A 876 ALA LEU VAL ALA ASP GLU ILE ALA GLU GLN ALA GLU PHE SEQRES 60 A 876 PHE SER PHE GLY THR ASN ASP LEU THR GLN MET THR PHE SEQRES 61 A 876 GLY TYR SER ARG ASP ASP VAL GLY LYS PHE ILE PRO VAL SEQRES 62 A 876 TYR LEU ALA GLN GLY ILE LEU GLN HIS ASP PRO PHE GLU SEQRES 63 A 876 VAL LEU ASP GLN ARG GLY VAL GLY GLU LEU VAL LYS PHE SEQRES 64 A 876 ALA THR GLU ARG GLY ARG LYS ALA ARG PRO ASN LEU LYS SEQRES 65 A 876 VAL GLY ILE CYS GLY GLU HIS GLY GLY GLU PRO SER SER SEQRES 66 A 876 VAL ALA PHE PHE ALA LYS ALA GLY LEU ASP TYR VAL SER SEQRES 67 A 876 CYS SER PRO PHE ARG VAL PRO ILE ALA ARG LEU ALA ALA SEQRES 68 A 876 ALA GLN VAL LEU VAL HET MG A2000 1 HET SO4 A3000 5 HET SO4 A3001 5 HET SO4 A3002 5 HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION FORMUL 2 MG MG 2+ FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *248(H2 O) HELIX 1 1 LEU A 24 ILE A 37 1 14 HELIX 2 2 SER A 48 ALA A 58 1 11 HELIX 3 3 GLY A 65 GLY A 82 1 18 HELIX 4 4 ASN A 117 GLY A 129 1 13 HELIX 5 5 GLY A 129 VAL A 148 1 20 HELIX 6 6 PRO A 152 GLY A 168 1 17 HELIX 7 7 ASN A 171 LEU A 175 5 5 HELIX 8 8 THR A 176 GLY A 196 1 21 HELIX 9 9 ASP A 202 TRP A 218 1 17 HELIX 10 10 SER A 220 ILE A 229 1 10 HELIX 11 11 GLN A 280 GLY A 287 1 8 HELIX 12 12 LEU A 294 MET A 301 1 8 HELIX 13 13 MET A 301 LYS A 320 1 20 HELIX 14 14 THR A 345 GLU A 359 1 15 HELIX 15 15 GLU A 363 ILE A 368 1 6 HELIX 16 16 LYS A 369 VAL A 371 5 3 HELIX 17 17 GLU A 372 LEU A 379 1 8 HELIX 18 18 ASN A 386 LYS A 391 5 6 HELIX 19 19 THR A 413 GLN A 423 1 11 HELIX 20 20 ASP A 438 ALA A 445 1 8 HELIX 21 21 SER A 457 TRP A 466 1 10 HELIX 22 22 GLY A 522 ARG A 535 1 14 HELIX 23 23 THR A 545 ASN A 555 1 11 HELIX 24 24 THR A 565 PHE A 570 1 6 HELIX 25 25 SER A 572 ALA A 585 1 14 HELIX 26 26 THR A 587 MET A 613 1 27 HELIX 27 27 PRO A 626 LEU A 631 5 6 HELIX 28 28 ASN A 635 GLY A 648 1 14 HELIX 29 29 ASN A 650 SER A 662 1 13 HELIX 30 30 ASN A 665 GLY A 669 5 5 HELIX 31 31 GLY A 672 TYR A 679 1 8 HELIX 32 32 TYR A 679 ASN A 699 1 21 HELIX 33 33 THR A 715 GLY A 738 1 24 HELIX 34 34 ILE A 751 VAL A 757 1 7 HELIX 35 35 VAL A 757 ALA A 762 1 6 HELIX 36 36 GLY A 771 GLY A 781 1 11 HELIX 37 37 ASP A 786 LYS A 789 5 4 HELIX 38 38 PHE A 790 GLN A 797 1 8 HELIX 39 39 GLY A 812 ARG A 828 1 17 HELIX 40 40 GLU A 838 GLY A 841 5 4 HELIX 41 41 GLU A 842 ALA A 852 1 11 HELIX 42 42 SER A 860 PHE A 862 5 3 HELIX 43 43 ARG A 863 VAL A 874 1 12 SHEET 1 A 6 LYS A 13 SER A 14 0 SHEET 2 A 6 VAL A 6 GLY A 10 -1 N GLY A 10 O LYS A 13 SHEET 3 A 6 GLY A 44 VAL A 47 -1 O THR A 46 N PHE A 7 SHEET 4 A 6 VAL A 240 CYS A 244 -1 O VAL A 242 N PHE A 45 SHEET 5 A 6 LEU A 94 ARG A 97 -1 N ARG A 97 O ASN A 241 SHEET 6 A 6 VAL A 111 LEU A 114 -1 O LEU A 114 N LEU A 94 SHEET 1 B 5 GLU A 292 ASP A 293 0 SHEET 2 B 5 TYR A 272 VAL A 277 -1 N PHE A 275 O GLU A 292 SHEET 3 B 5 GLY A 255 PHE A 260 -1 N PHE A 260 O TYR A 272 SHEET 4 B 5 GLN A 323 GLN A 330 -1 O VAL A 329 N GLY A 255 SHEET 5 B 5 ARG A 333 THR A 341 -1 O ARG A 340 N ASP A 324 SHEET 1 C 8 VAL A 394 THR A 397 0 SHEET 2 C 8 GLU A 507 LEU A 510 -1 O VAL A 508 N ALA A 396 SHEET 3 C 8 TRP A 498 ASN A 502 -1 N SER A 500 O ILE A 509 SHEET 4 C 8 ALA A 405 VAL A 411 -1 N ALA A 406 O LEU A 501 SHEET 5 C 8 ALA A 427 ARG A 431 1 O VAL A 430 N VAL A 411 SHEET 6 C 8 GLY A 447 THR A 450 1 O LEU A 449 N LEU A 429 SHEET 7 C 8 CYS A 470 SER A 472 1 O VAL A 471 N ILE A 448 SHEET 8 C 8 LEU A 399 SER A 402 -1 N LEU A 399 O SER A 472 SHEET 1 D 3 ILE A 477 ASN A 480 0 SHEET 2 D 3 LEU A 485 ILE A 488 -1 O LEU A 485 N ASN A 480 SHEET 3 D 3 HIS A 491 ARG A 494 -1 O HIS A 491 N ILE A 488 SHEET 1 E 9 LYS A 538 ASN A 542 0 SHEET 2 E 9 ILE A 560 ARG A 564 1 O GLY A 561 N ALA A 541 SHEET 3 E 9 PRO A 617 ARG A 621 1 O THR A 619 N ILE A 560 SHEET 4 E 9 PHE A 705 VAL A 710 1 O GLU A 707 N ILE A 620 SHEET 5 E 9 LYS A 744 ILE A 749 1 O GLY A 746 N ILE A 708 SHEET 6 E 9 PHE A 767 PHE A 770 1 O SER A 769 N THR A 747 SHEET 7 E 9 LYS A 832 CYS A 836 1 O LYS A 832 N PHE A 768 SHEET 8 E 9 TYR A 856 CYS A 859 1 O SER A 858 N ILE A 835 SHEET 9 E 9 LYS A 538 ASN A 542 1 N LEU A 540 O VAL A 857 LINK OE1 GLU A 750 MG MG A2000 1555 1555 2.14 LINK OD2 ASP A 774 MG MG A2000 1555 1555 1.99 LINK MG MG A2000 O HOH A3003 1555 1555 2.24 LINK MG MG A2000 O HOH A3008 1555 1555 2.15 LINK MG MG A2000 O HOH A3017 1555 1555 2.35 LINK MG MG A2000 O HOH A3020 1555 1555 2.19 SITE 1 AC1 6 GLU A 750 ASP A 774 HOH A3003 HOH A3008 SITE 2 AC1 6 HOH A3017 HOH A3020 SITE 1 AC2 10 ARG A 564 ARG A 621 HOH A3008 HOH A3017 SITE 2 AC2 10 HOH A3024 HOH A3175 HOH A3179 HOH A3184 SITE 3 AC2 10 HOH A3232 HOH A3243 SITE 1 AC3 8 ASN A 542 ARG A 564 GLY A 837 GLU A 838 SITE 2 AC3 8 SER A 860 HOH A3055 HOH A3185 HOH A3232 SITE 1 AC4 3 ALA A 519 LEU A 520 SER A 521 CRYST1 108.157 100.222 108.406 90.00 96.53 90.00 C 1 2 1 4 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 0.009246 0.000000 0.001058 0.00000 SCALE2 0.000000 0.009978 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009285 0.00000