HEADER LYASE 17-AUG-12 4GNL TITLE STRUCTURE OF RAT CYTOSOLIC PEPCK LD_2G IN COMPLEX WITH PEP AND GDP 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 4GNL 1 REMARK SEQADV LINK REVDAT 3 15-NOV-17 4GNL 1 REMARK REVDAT 2 26-JUL-17 4GNL 1 SOURCE REMARK REVDAT 1 03-JUL-13 4GNL 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 68107 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3448 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4097 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE SET COUNT : 215 REMARK 3 BIN FREE R VALUE : 0.3480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4748 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 374 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.82 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): 0.115 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.115 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.561 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4955 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6729 ; 1.527 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 617 ; 5.976 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 222 ;35.225 ;24.279 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 845 ;13.920 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;19.452 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 703 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3807 ; 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: REMARK 3 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4GNL 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_1000074408. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-12 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) : 1.15 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 : 68183 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.95200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 3DTB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22-26% PEG3350, 0.1 M HEPES, PH 7.4, REMARK 280 10 MM MANGANESE CHLORIDE, 10 MM GDP, 10 MM PEP, VAPOR DIFFUSION, REMARK 280 HANGING 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 30.62750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.48100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.37600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.48100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.62750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.37600 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 465 PRO A 3 REMARK 465 GLN A 4 REMARK 465 LEU A 5 REMARK 465 HIS A 6 REMARK 465 ASN A 7 REMARK 465 GLY A 8 REMARK 465 LEU A 9 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 O1B GDP A 704 O HOH A 802 1.90 REMARK 500 OG SER A 422 OE2 GLU A 424 2.14 REMARK 500 OG1 THR A 291 O HOH A 801 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 253 NE - CZ - NH2 ANGL. DEV. = -3.1 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 243 -74.83 -63.59 REMARK 500 TRP A 260 -165.64 -125.09 REMARK 500 ASP A 311 -52.85 -142.49 REMARK 500 PHE A 333 77.14 -111.34 REMARK 500 PHE A 480 16.23 59.01 REMARK 500 ALA A 505 -2.54 76.49 REMARK 500 PHE A 530 -128.28 51.58 REMARK 500 ASP A 562 -3.04 77.23 REMARK 500 ASN A 601 -112.71 38.80 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 703 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 79 O REMARK 620 2 ASN A 208 O 102.2 REMARK 620 3 HOH A 880 O 102.3 90.6 REMARK 620 4 HOH A 886 O 102.7 155.0 82.8 REMARK 620 5 HOH A1082 O 106.7 77.8 150.5 96.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 701 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 244 NZ REMARK 620 2 HIS A 264 NE2 85.0 REMARK 620 3 ASP A 311 OD1 98.5 89.0 REMARK 620 4 HOH A 803 O 87.4 89.8 173.9 REMARK 620 5 HOH A 804 O 94.2 179.1 91.3 90.0 REMARK 620 6 HOH A 805 O 170.5 91.0 90.0 84.0 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 702 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1145 O REMARK 620 2 HOH A1146 O 79.3 REMARK 620 3 HOH A1147 O 76.8 154.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEP A 705 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GMM RELATED DB: PDB REMARK 900 STRUCTURE OF RAT CYTOSOLIC PEPCK LD_1G IN COMPLEX WITH REMARK 900 SULFOPYRUVATE AND GTP 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: 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 GG LINKER. DBREF 4GNL A 1 463 UNP P07379 PCKGC_RAT 1 463 DBREF 4GNL A 475 622 UNP P07379 PCKGC_RAT 475 622 SEQADV 4GNL GLY A 464 UNP P07379 LINKER SEQADV 4GNL GLY A 465 UNP P07379 LINKER SEQRES 1 A 613 MET PRO PRO GLN LEU HIS ASN GLY LEU ASP PHE SER ALA SEQRES 2 A 613 LYS VAL ILE GLN GLY SER LEU ASP SER LEU PRO GLN GLU SEQRES 3 A 613 VAL ARG LYS PHE VAL GLU GLY ASN ALA GLN LEU CYS GLN SEQRES 4 A 613 PRO GLU TYR ILE HIS ILE CYS ASP GLY SER GLU GLU GLU SEQRES 5 A 613 TYR GLY ARG LEU LEU ALA HIS MET GLN GLU GLU GLY VAL SEQRES 6 A 613 ILE ARG LYS LEU LYS LYS TYR ASP ASN CYS TRP LEU ALA SEQRES 7 A 613 LEU THR ASP PRO ARG ASP VAL ALA ARG ILE GLU SER LYS SEQRES 8 A 613 THR VAL ILE ILE THR GLN GLU GLN ARG ASP THR VAL PRO SEQRES 9 A 613 ILE PRO LYS SER GLY GLN SER GLN LEU GLY ARG TRP MET SEQRES 10 A 613 SER GLU GLU ASP PHE GLU LYS ALA PHE ASN ALA ARG PHE SEQRES 11 A 613 PRO GLY CYS MET LYS GLY ARG THR MET TYR VAL ILE PRO SEQRES 12 A 613 PHE SER MET GLY PRO LEU GLY SER PRO LEU ALA LYS ILE SEQRES 13 A 613 GLY ILE GLU LEU THR ASP SER PRO TYR VAL VAL ALA SER SEQRES 14 A 613 MET ARG ILE MET THR ARG MET GLY THR SER VAL LEU GLU SEQRES 15 A 613 ALA LEU GLY ASP GLY GLU PHE ILE LYS CYS LEU HIS SER SEQRES 16 A 613 VAL GLY CYS PRO LEU PRO LEU LYS LYS PRO LEU VAL ASN SEQRES 17 A 613 ASN TRP ALA CYS ASN PRO GLU LEU THR LEU ILE ALA HIS SEQRES 18 A 613 LEU PRO ASP ARG ARG GLU ILE ILE SER PHE GLY SER GLY SEQRES 19 A 613 TYR GLY GLY ASN SER LEU LEU GLY LYS LYS CYS PHE ALA SEQRES 20 A 613 LEU ARG ILE ALA SER ARG LEU ALA LYS GLU GLU GLY TRP SEQRES 21 A 613 LEU ALA GLU HIS MET LEU ILE LEU GLY ILE THR ASN PRO SEQRES 22 A 613 GLU GLY LYS LYS LYS TYR LEU ALA ALA ALA PHE PRO SER SEQRES 23 A 613 ALA CYS GLY LYS THR ASN LEU ALA MET MET ASN PRO THR SEQRES 24 A 613 LEU PRO GLY TRP LYS VAL GLU CYS VAL GLY ASP ASP ILE SEQRES 25 A 613 ALA TRP MET LYS PHE ASP ALA GLN GLY ASN LEU ARG ALA SEQRES 26 A 613 ILE ASN PRO GLU ASN GLY PHE PHE GLY VAL ALA PRO GLY SEQRES 27 A 613 THR SER VAL LYS THR ASN PRO ASN ALA ILE LYS THR ILE SEQRES 28 A 613 GLN LYS ASN THR ILE PHE THR ASN VAL ALA GLU THR SER SEQRES 29 A 613 ASP GLY GLY VAL TYR TRP GLU GLY ILE ASP GLU PRO LEU SEQRES 30 A 613 ALA PRO GLY VAL THR ILE THR SER TRP LYS ASN LYS GLU SEQRES 31 A 613 TRP ARG PRO GLN ASP GLU GLU PRO CYS ALA HIS PRO ASN SEQRES 32 A 613 SER ARG PHE CYS THR PRO ALA SER GLN CYS PRO ILE ILE SEQRES 33 A 613 ASP PRO ALA TRP GLU SER PRO GLU GLY VAL PRO ILE GLU SEQRES 34 A 613 GLY ILE ILE PHE GLY GLY ARG ARG PRO ALA GLY VAL PRO SEQRES 35 A 613 LEU VAL TYR GLU ALA LEU SER TRP GLN HIS GLY VAL PHE SEQRES 36 A 613 VAL GLY ALA ALA MET ARG SER GLU GLY GLY ILE MET HIS SEQRES 37 A 613 ASP PRO PHE ALA MET ARG PRO PHE PHE GLY TYR ASN PHE SEQRES 38 A 613 GLY LYS TYR LEU ALA HIS TRP LEU SER MET ALA HIS ARG SEQRES 39 A 613 PRO ALA ALA LYS LEU PRO LYS ILE PHE HIS VAL ASN TRP SEQRES 40 A 613 PHE ARG LYS ASP LYS ASN GLY LYS PHE LEU TRP PRO GLY SEQRES 41 A 613 PHE GLY GLU ASN SER ARG VAL LEU GLU TRP MET PHE GLY SEQRES 42 A 613 ARG ILE GLU GLY GLU ASP SER ALA LYS LEU THR PRO ILE SEQRES 43 A 613 GLY TYR VAL PRO LYS GLU ASP ALA LEU ASN LEU LYS GLY SEQRES 44 A 613 LEU GLY ASP VAL ASN VAL GLU GLU LEU PHE GLY ILE SER SEQRES 45 A 613 LYS GLU PHE TRP GLU LYS GLU VAL GLU GLU ILE ASP LYS SEQRES 46 A 613 TYR LEU GLU ASP GLN VAL ASN ALA ASP LEU PRO TYR GLU SEQRES 47 A 613 ILE GLU ARG GLU LEU ARG ALA LEU LYS GLN ARG ILE SER SEQRES 48 A 613 GLN MET HET MN A 701 1 HET MN A 702 1 HET NA A 703 1 HET GDP A 704 28 HET PEP A 705 10 HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM PEP PHOSPHOENOLPYRUVATE FORMUL 2 MN 2(MN 2+) FORMUL 4 NA NA 1+ FORMUL 5 GDP C10 H15 N5 O11 P2 FORMUL 6 PEP C3 H5 O6 P FORMUL 7 HOH *374(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 SER A 462 ILE A 475 5 5 HELIX 19 19 ASP A 478 MET A 482 5 5 HELIX 20 20 ASN A 489 MET A 500 1 12 HELIX 21 21 ALA A 501 ARG A 503 5 3 HELIX 22 22 GLY A 529 GLU A 532 5 4 HELIX 23 23 ASN A 533 GLU A 545 1 13 HELIX 24 24 ASN A 573 PHE A 578 1 6 HELIX 25 25 SER A 581 VAL A 600 1 20 HELIX 26 26 ASN A 601 LEU A 604 5 4 HELIX 27 27 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 MET A 139 N TYR A 42 SHEET 4 A 9 LYS A 155 THR A 161 -1 O THR A 161 N TYR A 140 SHEET 5 A 9 ILE A 190 SER A 195 1 O CYS A 192 N LEU A 160 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 ILE A 95 O HIS A 221 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 MET A 139 N TYR A 42 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 PHE A 332 O THR A 408 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 ILE A 326 N TRP A 314 SHEET 4 D 7 VAL A 426 GLY A 435 -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 ILE A 326 N TRP A 314 SHEET 4 E 6 VAL A 426 GLY A 435 -1 O ILE A 428 N LEU A 323 SHEET 5 E 6 LYS A 510 ASN A 515 1 O PHE A 512 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 ALA A 550 THR A 553 0 SHEET 2 G 2 GLY A 556 PRO A 559 -1 O VAL A 558 N LYS A 551 LINK O LEU A 79 NA NA A 703 1555 1555 2.27 LINK O ASN A 208 NA NA A 703 1555 1555 2.19 LINK NZ LYS A 244 MN MN A 701 1555 1555 2.29 LINK NE2 HIS A 264 MN MN A 701 1555 1555 2.16 LINK OD1 ASP A 311 MN MN A 701 1555 1555 2.13 LINK MN MN A 701 O HOH A 803 1555 1555 2.22 LINK MN MN A 701 O HOH A 804 1555 1555 2.06 LINK MN MN A 701 O HOH A 805 1555 1555 2.13 LINK MN MN A 702 O HOH A1145 1555 1555 2.08 LINK MN MN A 702 O HOH A1146 1555 1555 1.95 LINK MN MN A 702 O HOH A1147 1555 1555 2.24 LINK NA NA A 703 O HOH A 880 1555 1555 2.34 LINK NA NA A 703 O HOH A 886 1555 1555 2.52 LINK NA NA A 703 O HOH A1082 1555 1555 2.41 CISPEP 1 LEU A 200 PRO A 201 0 1.83 SITE 1 AC1 6 LYS A 244 HIS A 264 ASP A 311 HOH A 803 SITE 2 AC1 6 HOH A 804 HOH A 805 SITE 1 AC2 4 THR A 291 HOH A1145 HOH A1146 HOH A1147 SITE 1 AC3 5 LEU A 79 ASN A 208 HOH A 880 HOH A 886 SITE 2 AC3 5 HOH A1082 SITE 1 AC4 21 PRO A 285 ALA A 287 CYS A 288 GLY A 289 SITE 2 AC4 21 LYS A 290 THR A 291 ASN A 292 ARG A 436 SITE 3 AC4 21 TRP A 516 PHE A 517 PHE A 525 GLY A 529 SITE 4 AC4 21 PHE A 530 ASN A 533 HOH A 801 HOH A 802 SITE 5 AC4 21 HOH A 843 HOH A 863 HOH A1057 HOH A1144 SITE 6 AC4 21 HOH A1147 SITE 1 AC5 13 ALA A 86 ARG A 87 TYR A 235 GLY A 236 SITE 2 AC5 13 GLY A 237 LYS A 244 ASN A 403 ARG A 405 SITE 3 AC5 13 PHE A 485 HOH A 803 HOH A 804 HOH A 806 SITE 4 AC5 13 HOH A 868 CRYST1 61.255 84.752 118.962 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 0.016325 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011799 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008406 0.00000