HEADER LYASE 16-AUG-12 4GMM
TITLE STRUCTURE OF RAT CYTOSOLIC PEPCK LD_1G IN COMPLEX WITH BETA-
TITLE 2 SULFOPYRUVATE AND GTP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC [GTP];
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: SEE REMARK 999;
COMPND 5 SYNONYM: PEPCK-C, PHOSPHOENOLPYRUVATE CARBOXYLASE;
COMPND 6 EC: 4.1.1.32;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;
SOURCE 3 ORGANISM_COMMON: RAT;
SOURCE 4 ORGANISM_TAXID: 10116;
SOURCE 5 GENE: PCK1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSUMO
KEYWDS KINASE, GLUCONEOGENESIS, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR T.A.JOHNSON,T.HOLYOAK
REVDAT 4 13-SEP-23 4GMM 1 REMARK SEQADV LINK
REVDAT 3 15-NOV-17 4GMM 1 REMARK
REVDAT 2 26-JUL-17 4GMM 1 SOURCE REMARK
REVDAT 1 03-JUL-13 4GMM 0
JRNL AUTH T.A.JOHNSON,T.HOLYOAK
JRNL TITL THE {OMEGA}-LOOP LID DOMAIN OF PHOSPHOENOLPYRUVATE
JRNL TITL 2 CARBOXYKINASE IS ESSENTIAL FOR CATALYTIC FUNCTION.
JRNL REF BIOCHEMISTRY V. 51 9547 2012
JRNL REFN ISSN 0006-2960
JRNL PMID 23127136
JRNL DOI 10.1021/BI301278T
REMARK 2
REMARK 2 RESOLUTION. 1.74 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.36
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0
REMARK 3 NUMBER OF REFLECTIONS : 59098
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 + TEST SET) : 0.189
REMARK 3 R VALUE (WORKING SET) : 0.187
REMARK 3 FREE R VALUE : 0.224
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 3138
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.74
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3390
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.71
REMARK 3 BIN R VALUE (WORKING SET) : 0.3130
REMARK 3 BIN FREE R VALUE SET COUNT : 174
REMARK 3 BIN FREE R VALUE : 0.3600
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4798
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 45
REMARK 3 SOLVENT ATOMS : 412
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.39
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.00000
REMARK 3 B22 (A**2) : 0.00000
REMARK 3 B33 (A**2) : 0.00000
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 OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.126
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.120
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.961
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5082 ; 0.013 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6916 ; 1.628 ; 1.972
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 637 ; 6.296 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 232 ;34.588 ;24.310
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 872 ;14.458 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;16.396 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 721 ; 0.101 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3918 ; 0.008 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN
REMARK 3 THE INPUT
REMARK 4
REMARK 4 4GMM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-AUG-12.
REMARK 100 THE DEPOSITION ID IS D_1000074373.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 02-MAR-11
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRL
REMARK 200 BEAMLINE : BL7-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9
REMARK 200 MONOCHROMATOR : SIDE SCATTERING BENT CUBE-ROOT I
REMARK 200 -BEAM SINGLE CRYSTAL, ASYMMETRIC
REMARK 200 CUT 4.965 DEGREES
REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING),
REMARK 200 SINGLE CRYSTAL SI(111) BENT
REMARK 200 MONOCHROMATOR (HORIZONTAL
REMARK 200 FOCUSING)
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62571
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.736
REMARK 200 RESOLUTION RANGE LOW (A) : 100.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6
REMARK 200 DATA REDUNDANCY : 3.800
REMARK 200 R MERGE (I) : 0.08300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.70
REMARK 200 R MERGE FOR SHELL (I) : 0.79500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 3DT7
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.92
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 22-26% PEG3350, 0.1 M HEPES, PH 7.4,
REMARK 280 10 MM MANGANESE CHLORIDE, 10 MM GTP, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
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 30.29900
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.54200
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.38700
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.54200
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.29900
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.38700
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 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 1
REMARK 465 PRO A 2
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 OH TYR A 42 O HOH A 1039 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 HIS A 452 CG HIS A 452 CD2 0.064
REMARK 500 HIS A 477 CG HIS A 477 CD2 0.062
REMARK 500 TRP A 539 CE2 TRP A 539 CD2 0.073
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 HIS A 6 -108.17 -123.11
REMARK 500 ARG A 129 -54.55 -126.95
REMARK 500 LEU A 218 118.19 -161.10
REMARK 500 LYS A 243 -75.44 -76.33
REMARK 500 TRP A 260 -167.56 -120.58
REMARK 500 SER A 286 139.77 -39.75
REMARK 500 ASP A 311 -37.54 -150.06
REMARK 500 PHE A 333 72.90 -110.38
REMARK 500 ASN A 344 68.63 -163.27
REMARK 500 PRO A 393 -7.07 -53.56
REMARK 500 PHE A 480 15.46 58.96
REMARK 500 PHE A 530 -124.05 55.83
REMARK 500 ASP A 562 -6.71 80.59
REMARK 500 ASN A 601 -110.20 38.37
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 NA A 702 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LEU A 79 O
REMARK 620 2 ASN A 208 O 100.8
REMARK 620 3 HOH A 804 O 99.1 89.2
REMARK 620 4 HOH A 805 O 101.1 157.2 93.5
REMARK 620 5 HOH A1055 O 105.6 82.8 155.0 85.3
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 703 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LYS A 244 NZ
REMARK 620 2 HIS A 264 NE2 80.7
REMARK 620 3 ASP A 311 OD1 96.9 91.9
REMARK 620 4 GTP A 701 O2G 174.5 94.7 86.1
REMARK 620 5 SPV A 705 O1 91.3 95.9 169.5 86.2
REMARK 620 6 SPV A 705 O2 88.1 165.3 98.8 96.0 74.9
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 704 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 THR A 291 OG1
REMARK 620 2 GTP A 701 O2B 87.2
REMARK 620 3 GTP A 701 O1G 177.2 92.8
REMARK 620 4 HOH A 801 O 85.3 86.7 91.9
REMARK 620 5 HOH A 802 O 83.5 169.2 96.8 97.9
REMARK 620 6 HOH A 803 O 92.7 87.9 90.1 174.3 87.2
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 GTP A 701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 702
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 703
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 704
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPV A 705
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4GMU RELATED DB: PDB
REMARK 900 STRUCTURE OF RAT CYTOSOLIC PEPCK LD_1G IN COMPLEX WITH OXALATE AND
REMARK 900 GTP
REMARK 900 RELATED ID: 4GMW RELATED DB: PDB
REMARK 900 STRUCTURE OF RAT CYTOSOLIC PEPCK LD_1G IN COMPLEX WITH PEP AND GDP
REMARK 900 RELATED ID: 4GMZ RELATED DB: PDB
REMARK 900 STRUCTURE OF RAT CYTOSOLIC PEPCK LD_2G IN COMPLEX WITH
REMARK 900 SULFOPYRUVATE AND GTP
REMARK 900 RELATED ID: 4GNL RELATED DB: PDB
REMARK 900 STRUCTURE OF RAT CYTOSOLIC PEPCK LD_2G IN COMPLEX WITH PEP AND GDP
REMARK 900 RELATED ID: 4GNM RELATED DB: PDB
REMARK 900 STRUCTURE OF RAT CYTOSOLIC PEPCK LD_2G IN COMPLEX WITH OXALATE AND
REMARK 900 GTP
REMARK 900 RELATED ID: 4GNO RELATED DB: PDB
REMARK 900 STRUCTURE OF RAT CYTOSOLIC PEPCK LD_3G IN COMPLEX WITH
REMARK 900 SULFOPYRUVATE AND GTP
REMARK 900 RELATED ID: 4GNP RELATED DB: PDB
REMARK 900 STRUCTURE OF RAT CYTOSOLIC PEPCK LD_3G IN COMPLEX WITH PEP AND GDP
REMARK 900 RELATED ID: 4GNQ RELATED DB: PDB
REMARK 900 STRUCTURE OF RAT CYTOSOLIC PEPCK LD_3G IN COMPLEX WITH OXALATE AND
REMARK 900 GTP
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 RESIDUES 464-474 (ATAAAEHKGKV) OF PEPCK HAVE BEEN DELETED AND
REMARK 999 REPLACED BY A G LINKER.
DBREF 4GMM A 1 463 UNP P07379 PCKGC_RAT 1 463
DBREF 4GMM A 475 622 UNP P07379 PCKGC_RAT 475 622
SEQADV 4GMM GLY A 464 UNP P07379 LINKER
SEQRES 1 A 612 MET PRO PRO GLN LEU HIS ASN GLY LEU ASP PHE SER ALA
SEQRES 2 A 612 LYS VAL ILE GLN GLY SER LEU ASP SER LEU PRO GLN GLU
SEQRES 3 A 612 VAL ARG LYS PHE VAL GLU GLY ASN ALA GLN LEU CYS GLN
SEQRES 4 A 612 PRO GLU TYR ILE HIS ILE CYS ASP GLY SER GLU GLU GLU
SEQRES 5 A 612 TYR GLY ARG LEU LEU ALA HIS MET GLN GLU GLU GLY VAL
SEQRES 6 A 612 ILE ARG LYS LEU LYS LYS TYR ASP ASN CYS TRP LEU ALA
SEQRES 7 A 612 LEU THR ASP PRO ARG ASP VAL ALA ARG ILE GLU SER LYS
SEQRES 8 A 612 THR VAL ILE ILE THR GLN GLU GLN ARG ASP THR VAL PRO
SEQRES 9 A 612 ILE PRO LYS SER GLY GLN SER GLN LEU GLY ARG TRP MET
SEQRES 10 A 612 SER GLU GLU ASP PHE GLU LYS ALA PHE ASN ALA ARG PHE
SEQRES 11 A 612 PRO GLY CYS MET LYS GLY ARG THR MET TYR VAL ILE PRO
SEQRES 12 A 612 PHE SER MET GLY PRO LEU GLY SER PRO LEU ALA LYS ILE
SEQRES 13 A 612 GLY ILE GLU LEU THR ASP SER PRO TYR VAL VAL ALA SER
SEQRES 14 A 612 MET ARG ILE MET THR ARG MET GLY THR SER VAL LEU GLU
SEQRES 15 A 612 ALA LEU GLY ASP GLY GLU PHE ILE LYS CYS LEU HIS SER
SEQRES 16 A 612 VAL GLY CYS PRO LEU PRO LEU LYS LYS PRO LEU VAL ASN
SEQRES 17 A 612 ASN TRP ALA CYS ASN PRO GLU LEU THR LEU ILE ALA HIS
SEQRES 18 A 612 LEU PRO ASP ARG ARG GLU ILE ILE SER PHE GLY SER GLY
SEQRES 19 A 612 TYR GLY GLY ASN SER LEU LEU GLY LYS LYS CYS PHE ALA
SEQRES 20 A 612 LEU ARG ILE ALA SER ARG LEU ALA LYS GLU GLU GLY TRP
SEQRES 21 A 612 LEU ALA GLU HIS MET LEU ILE LEU GLY ILE THR ASN PRO
SEQRES 22 A 612 GLU GLY LYS LYS LYS TYR LEU ALA ALA ALA PHE PRO SER
SEQRES 23 A 612 ALA CYS GLY LYS THR ASN LEU ALA MET MET ASN PRO THR
SEQRES 24 A 612 LEU PRO GLY TRP LYS VAL GLU CYS VAL GLY ASP ASP ILE
SEQRES 25 A 612 ALA TRP MET LYS PHE ASP ALA GLN GLY ASN LEU ARG ALA
SEQRES 26 A 612 ILE ASN PRO GLU ASN GLY PHE PHE GLY VAL ALA PRO GLY
SEQRES 27 A 612 THR SER VAL LYS THR ASN PRO ASN ALA ILE LYS THR ILE
SEQRES 28 A 612 GLN LYS ASN THR ILE PHE THR ASN VAL ALA GLU THR SER
SEQRES 29 A 612 ASP GLY GLY VAL TYR TRP GLU GLY ILE ASP GLU PRO LEU
SEQRES 30 A 612 ALA PRO GLY VAL THR ILE THR SER TRP LYS ASN LYS GLU
SEQRES 31 A 612 TRP ARG PRO GLN ASP GLU GLU PRO CYS ALA HIS PRO ASN
SEQRES 32 A 612 SER ARG PHE CYS THR PRO ALA SER GLN CYS PRO ILE ILE
SEQRES 33 A 612 ASP PRO ALA TRP GLU SER PRO GLU GLY VAL PRO ILE GLU
SEQRES 34 A 612 GLY ILE ILE PHE GLY GLY ARG ARG PRO ALA GLY VAL PRO
SEQRES 35 A 612 LEU VAL TYR GLU ALA LEU SER TRP GLN HIS GLY VAL PHE
SEQRES 36 A 612 VAL GLY ALA ALA MET ARG SER GLU GLY ILE MET HIS ASP
SEQRES 37 A 612 PRO PHE ALA MET ARG PRO PHE PHE GLY TYR ASN PHE GLY
SEQRES 38 A 612 LYS TYR LEU ALA HIS TRP LEU SER MET ALA HIS ARG PRO
SEQRES 39 A 612 ALA ALA LYS LEU PRO LYS ILE PHE HIS VAL ASN TRP PHE
SEQRES 40 A 612 ARG LYS ASP LYS ASN GLY LYS PHE LEU TRP PRO GLY PHE
SEQRES 41 A 612 GLY GLU ASN SER ARG VAL LEU GLU TRP MET PHE GLY ARG
SEQRES 42 A 612 ILE GLU GLY GLU ASP SER ALA LYS LEU THR PRO ILE GLY
SEQRES 43 A 612 TYR VAL PRO LYS GLU ASP ALA LEU ASN LEU LYS GLY LEU
SEQRES 44 A 612 GLY ASP VAL ASN VAL GLU GLU LEU PHE GLY ILE SER LYS
SEQRES 45 A 612 GLU PHE TRP GLU LYS GLU VAL GLU GLU ILE ASP LYS TYR
SEQRES 46 A 612 LEU GLU ASP GLN VAL ASN ALA ASP LEU PRO TYR GLU ILE
SEQRES 47 A 612 GLU ARG GLU LEU ARG ALA LEU LYS GLN ARG ILE SER GLN
SEQRES 48 A 612 MET
HET GTP A 701 32
HET NA A 702 1
HET MN A 703 1
HET MN A 704 1
HET SPV A 705 10
HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE
HETNAM NA SODIUM ION
HETNAM MN MANGANESE (II) ION
HETNAM SPV SULFOPYRUVATE
FORMUL 2 GTP C10 H16 N5 O14 P3
FORMUL 3 NA NA 1+
FORMUL 4 MN 2(MN 2+)
FORMUL 6 SPV C3 H4 O6 S
FORMUL 7 HOH *412(H2 O)
HELIX 1 1 PHE A 11 ALA A 13 5 3
HELIX 2 2 SER A 19 LEU A 23 5 5
HELIX 3 3 PRO A 24 GLN A 39 1 16
HELIX 4 4 SER A 49 GLU A 63 1 15
HELIX 5 5 ILE A 88 SER A 90 5 3
HELIX 6 6 GLU A 98 VAL A 103 1 6
HELIX 7 7 SER A 118 ALA A 128 1 11
HELIX 8 8 SER A 163 THR A 174 1 12
HELIX 9 9 GLY A 177 GLY A 185 1 9
HELIX 10 10 ASN A 213 THR A 217 5 5
HELIX 11 11 PRO A 223 ARG A 225 5 3
HELIX 12 12 TYR A 235 LEU A 240 1 6
HELIX 13 13 LEU A 248 GLY A 259 1 12
HELIX 14 14 GLY A 289 MET A 295 1 7
HELIX 15 15 ASN A 344 ILE A 351 1 8
HELIX 16 16 SER A 411 CYS A 413 5 3
HELIX 17 17 SER A 449 ALA A 459 1 11
HELIX 18 18 PRO A 479 MET A 482 5 4
HELIX 19 19 ASN A 489 MET A 500 1 12
HELIX 20 20 ALA A 501 ARG A 503 5 3
HELIX 21 21 GLY A 529 GLU A 532 5 4
HELIX 22 22 ASN A 533 GLU A 545 1 13
HELIX 23 23 ASN A 573 PHE A 578 1 6
HELIX 24 24 SER A 581 VAL A 600 1 20
HELIX 25 25 ASN A 601 LEU A 604 5 4
HELIX 26 26 PRO A 605 GLN A 621 1 17
SHEET 1 A 9 VAL A 15 GLN A 17 0
SHEET 2 A 9 TYR A 42 ILE A 45 1 O ILE A 43 N ILE A 16
SHEET 3 A 9 THR A 138 MET A 146 1 O VAL A 141 N HIS A 44
SHEET 4 A 9 LYS A 155 THR A 161 -1 O LYS A 155 N MET A 146
SHEET 5 A 9 ILE A 190 SER A 195 1 O CYS A 192 N ILE A 158
SHEET 6 A 9 GLU A 227 PHE A 231 1 O SER A 230 N LEU A 193
SHEET 7 A 9 LEU A 218 LEU A 222 -1 N LEU A 222 O GLU A 227
SHEET 8 A 9 THR A 92 ILE A 95 1 N VAL A 93 O ILE A 219
SHEET 9 A 9 TRP A 116 MET A 117 1 O MET A 117 N ILE A 94
SHEET 1 B 4 VAL A 15 GLN A 17 0
SHEET 2 B 4 TYR A 42 ILE A 45 1 O ILE A 43 N ILE A 16
SHEET 3 B 4 THR A 138 MET A 146 1 O VAL A 141 N HIS A 44
SHEET 4 B 4 ARG A 175 MET A 176 -1 O ARG A 175 N SER A 145
SHEET 1 C 5 ARG A 67 LYS A 68 0
SHEET 2 C 5 TRP A 76 ALA A 78 -1 O LEU A 77 N ARG A 67
SHEET 3 C 5 ILE A 356 THR A 358 1 O PHE A 357 N TRP A 76
SHEET 4 C 5 ARG A 405 PRO A 409 -1 O ARG A 405 N THR A 358
SHEET 5 C 5 GLY A 331 VAL A 335 -1 N GLY A 334 O PHE A 406
SHEET 1 D 7 LEU A 261 GLU A 263 0
SHEET 2 D 7 ALA A 313 PHE A 317 -1 O MET A 315 N LEU A 261
SHEET 3 D 7 LEU A 323 ILE A 326 -1 O ARG A 324 N LYS A 316
SHEET 4 D 7 VAL A 426 GLY A 434 -1 O ILE A 428 N LEU A 323
SHEET 5 D 7 LYS A 277 ALA A 283 1 N TYR A 279 O GLU A 429
SHEET 6 D 7 LEU A 266 THR A 271 -1 N ILE A 270 O LYS A 278
SHEET 7 D 7 LYS A 304 GLY A 309 -1 O GLU A 306 N GLY A 269
SHEET 1 E 6 LEU A 261 GLU A 263 0
SHEET 2 E 6 ALA A 313 PHE A 317 -1 O MET A 315 N LEU A 261
SHEET 3 E 6 LEU A 323 ILE A 326 -1 O ARG A 324 N LYS A 316
SHEET 4 E 6 VAL A 426 GLY A 434 -1 O ILE A 428 N LEU A 323
SHEET 5 E 6 LYS A 510 VAL A 514 1 O VAL A 514 N PHE A 433
SHEET 6 E 6 VAL A 444 GLU A 446 -1 N TYR A 445 O HIS A 513
SHEET 1 F 4 VAL A 368 TYR A 369 0
SHEET 2 F 4 ALA A 361 THR A 363 -1 N ALA A 361 O TYR A 369
SHEET 3 F 4 ILE A 383 THR A 384 -1 O THR A 384 N GLU A 362
SHEET 4 F 4 GLU A 390 TRP A 391 -1 O TRP A 391 N ILE A 383
SHEET 1 G 2 ARG A 461 GLU A 463 0
SHEET 2 G 2 MET A 476 HIS A 477 -1 O MET A 476 N SER A 462
SHEET 1 H 2 ALA A 550 THR A 553 0
SHEET 2 H 2 GLY A 556 PRO A 559 -1 O VAL A 558 N LYS A 551
LINK O LEU A 79 NA NA A 702 1555 1555 2.29
LINK O ASN A 208 NA NA A 702 1555 1555 2.13
LINK NZ LYS A 244 MN MN A 703 1555 1555 2.40
LINK NE2 HIS A 264 MN MN A 703 1555 1555 2.27
LINK OG1 THR A 291 MN MN A 704 1555 1555 2.23
LINK OD1 ASP A 311 MN MN A 703 1555 1555 2.13
LINK O2G GTP A 701 MN MN A 703 1555 1555 2.24
LINK O2B GTP A 701 MN MN A 704 1555 1555 2.14
LINK O1G GTP A 701 MN MN A 704 1555 1555 2.20
LINK NA NA A 702 O HOH A 804 1555 1555 2.18
LINK NA NA A 702 O HOH A 805 1555 1555 2.18
LINK NA NA A 702 O HOH A1055 1555 1555 2.33
LINK MN MN A 703 O1 SPV A 705 1555 1555 2.16
LINK MN MN A 703 O2 SPV A 705 1555 1555 2.28
LINK MN MN A 704 O HOH A 801 1555 1555 2.33
LINK MN MN A 704 O HOH A 802 1555 1555 2.20
LINK MN MN A 704 O HOH A 803 1555 1555 2.31
CISPEP 1 LEU A 200 PRO A 201 0 0.66
SITE 1 AC1 32 HIS A 264 PRO A 285 SER A 286 ALA A 287
SITE 2 AC1 32 CYS A 288 GLY A 289 LYS A 290 THR A 291
SITE 3 AC1 32 ASN A 292 ASP A 311 VAL A 335 ARG A 405
SITE 4 AC1 32 ARG A 436 TRP A 516 PHE A 517 PHE A 525
SITE 5 AC1 32 GLY A 529 PHE A 530 ASN A 533 MN A 703
SITE 6 AC1 32 MN A 704 SPV A 705 HOH A 801 HOH A 803
SITE 7 AC1 32 HOH A 842 HOH A 850 HOH A 873 HOH A 888
SITE 8 AC1 32 HOH A 967 HOH A1020 HOH A1021 HOH A1068
SITE 1 AC2 5 LEU A 79 ASN A 208 HOH A 804 HOH A 805
SITE 2 AC2 5 HOH A1055
SITE 1 AC3 5 LYS A 244 HIS A 264 ASP A 311 GTP A 701
SITE 2 AC3 5 SPV A 705
SITE 1 AC4 5 THR A 291 GTP A 701 HOH A 801 HOH A 802
SITE 2 AC4 5 HOH A 803
SITE 1 AC5 15 ARG A 87 GLY A 236 GLY A 237 LYS A 243
SITE 2 AC5 15 LYS A 244 HIS A 264 SER A 286 ASP A 311
SITE 3 AC5 15 PHE A 333 ARG A 405 GTP A 701 MN A 703
SITE 4 AC5 15 HOH A 809 HOH A 810 HOH A 814
CRYST1 60.598 84.774 119.084 90.00 90.00 90.00 P 21 21 21 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 0.016502 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011796 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008397 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
