HEADER LYASE 17-AUG-12 4GNQ TITLE STRUCTURE OF RAT CYTOSOLIC PEPCK LD_3G IN COMPLEX WITH OXALATE 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 3 13-SEP-23 4GNQ 1 REMARK SEQADV LINK REVDAT 2 26-JUL-17 4GNQ 1 SOURCE REMARK REVDAT 1 03-JUL-13 4GNQ 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. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 118896 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5982 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.43 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6922 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.3510 REMARK 3 BIN FREE R VALUE SET COUNT : 352 REMARK 3 BIN FREE R VALUE : 0.3920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4806 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 697 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.43 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): 0.063 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.064 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.077 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5236 ; 0.017 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7141 ; 1.914 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 677 ; 6.243 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 238 ;35.184 ;24.118 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 921 ;12.930 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;16.723 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 746 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4046 ; 0.012 ; 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 4GNQ 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_1000074413. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-10 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 119287 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 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 : 8.400 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.81700 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 3DT2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 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 30.24350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.48550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.16450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.48550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.24350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.16450 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 NZ LYS A 244 O HOH A 1497 1.83 REMARK 500 OG SER A 422 OE1 GLU A 424 2.06 REMARK 500 OE2 GLU A 41 O HOH A 989 2.07 REMARK 500 OE1 GLU A 89 O HOH A 1455 2.09 REMARK 500 CD1 PHE A 578 O HOH A 1195 2.12 REMARK 500 OE1 GLU A 63 O HOH A 1387 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 HIS A 502 O HOH A 1386 2454 2.00 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 194 CG HIS A 194 CD2 0.056 REMARK 500 HIS A 452 CG HIS A 452 CD2 0.080 REMARK 500 TRP A 527 CE2 TRP A 527 CD2 0.091 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 ASP A 47 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 55 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 171 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 PHE A 246 CB - CG - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 PHE A 246 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 461 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 461 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP A 520 CB - CG - OD1 ANGL. DEV. = 6.0 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 HIS A 6 -105.41 -127.38 REMARK 500 LEU A 9 35.17 -95.59 REMARK 500 ARG A 129 -54.21 -126.11 REMARK 500 LYS A 243 -84.58 -80.39 REMARK 500 ASP A 311 -45.21 -146.77 REMARK 500 PHE A 333 75.29 -105.32 REMARK 500 ASN A 344 67.75 -165.13 REMARK 500 PHE A 480 15.68 58.90 REMARK 500 ALA A 505 17.07 57.96 REMARK 500 PHE A 530 -127.60 52.58 REMARK 500 ASN A 601 -115.12 46.12 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 704 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 79 O REMARK 620 2 ASN A 208 O 101.4 REMARK 620 3 HOH A 955 O 98.2 160.0 REMARK 620 4 HOH A 983 O 100.3 89.1 83.5 REMARK 620 5 HOH A1086 O 108.0 85.1 92.6 151.7 REMARK 620 N 1 2 3 4 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 LYS A 244 NZ REMARK 620 2 HIS A 264 NE2 88.8 REMARK 620 3 ASP A 311 OD1 93.9 92.9 REMARK 620 4 GTP A 701 O1G 176.1 94.1 88.6 REMARK 620 5 OXL A 705 O2 86.0 98.8 168.3 90.9 REMARK 620 6 OXL A 705 O1 83.6 171.7 91.0 93.3 77.3 REMARK 620 7 HOH A1477 O 9.5 80.1 97.9 171.4 83.9 92.2 REMARK 620 N 1 2 3 4 5 6 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 THR A 291 OG1 REMARK 620 2 GTP A 701 O2G 178.7 REMARK 620 3 GTP A 701 O2B 88.6 92.2 REMARK 620 4 HOH A 821 O 84.2 95.0 172.1 REMARK 620 5 HOH A 850 O 85.9 93.2 86.1 96.6 REMARK 620 6 HOH A 855 O 92.5 88.5 88.9 88.2 174.7 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 GTP 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 MN A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXL 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: 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 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 464-474 (ATAAAEHKGKV) OF PEPCK HAVE BEEN DELETED AND REMARK 999 REPLACED BY A GGG LINKER. DBREF 4GNQ A 1 463 UNP P07379 PCKGC_RAT 1 463 DBREF 4GNQ A 475 622 UNP P07379 PCKGC_RAT 475 622 SEQADV 4GNQ GLY A 464 UNP P07379 LINKER SEQADV 4GNQ GLY A 465 UNP P07379 LINKER SEQADV 4GNQ GLY A 466 UNP P07379 LINKER SEQRES 1 A 614 MET PRO PRO GLN LEU HIS ASN GLY LEU ASP PHE SER ALA SEQRES 2 A 614 LYS VAL ILE GLN GLY SER LEU ASP SER LEU PRO GLN GLU SEQRES 3 A 614 VAL ARG LYS PHE VAL GLU GLY ASN ALA GLN LEU CYS GLN SEQRES 4 A 614 PRO GLU TYR ILE HIS ILE CYS ASP GLY SER GLU GLU GLU SEQRES 5 A 614 TYR GLY ARG LEU LEU ALA HIS MET GLN GLU GLU GLY VAL SEQRES 6 A 614 ILE ARG LYS LEU LYS LYS TYR ASP ASN CYS TRP LEU ALA SEQRES 7 A 614 LEU THR ASP PRO ARG ASP VAL ALA ARG ILE GLU SER LYS SEQRES 8 A 614 THR VAL ILE ILE THR GLN GLU GLN ARG ASP THR VAL PRO SEQRES 9 A 614 ILE PRO LYS SER GLY GLN SER GLN LEU GLY ARG TRP MET SEQRES 10 A 614 SER GLU GLU ASP PHE GLU LYS ALA PHE ASN ALA ARG PHE SEQRES 11 A 614 PRO GLY CYS MET LYS GLY ARG THR MET TYR VAL ILE PRO SEQRES 12 A 614 PHE SER MET GLY PRO LEU GLY SER PRO LEU ALA LYS ILE SEQRES 13 A 614 GLY ILE GLU LEU THR ASP SER PRO TYR VAL VAL ALA SER SEQRES 14 A 614 MET ARG ILE MET THR ARG MET GLY THR SER VAL LEU GLU SEQRES 15 A 614 ALA LEU GLY ASP GLY GLU PHE ILE LYS CYS LEU HIS SER SEQRES 16 A 614 VAL GLY CYS PRO LEU PRO LEU LYS LYS PRO LEU VAL ASN SEQRES 17 A 614 ASN TRP ALA CYS ASN PRO GLU LEU THR LEU ILE ALA HIS SEQRES 18 A 614 LEU PRO ASP ARG ARG GLU ILE ILE SER PHE GLY SER GLY SEQRES 19 A 614 TYR GLY GLY ASN SER LEU LEU GLY LYS LYS CYS PHE ALA SEQRES 20 A 614 LEU ARG ILE ALA SER ARG LEU ALA LYS GLU GLU GLY TRP SEQRES 21 A 614 LEU ALA GLU HIS MET LEU ILE LEU GLY ILE THR ASN PRO SEQRES 22 A 614 GLU GLY LYS LYS LYS TYR LEU ALA ALA ALA PHE PRO SER SEQRES 23 A 614 ALA CYS GLY LYS THR ASN LEU ALA MET MET ASN PRO THR SEQRES 24 A 614 LEU PRO GLY TRP LYS VAL GLU CYS VAL GLY ASP ASP ILE SEQRES 25 A 614 ALA TRP MET LYS PHE ASP ALA GLN GLY ASN LEU ARG ALA SEQRES 26 A 614 ILE ASN PRO GLU ASN GLY PHE PHE GLY VAL ALA PRO GLY SEQRES 27 A 614 THR SER VAL LYS THR ASN PRO ASN ALA ILE LYS THR ILE SEQRES 28 A 614 GLN LYS ASN THR ILE PHE THR ASN VAL ALA GLU THR SER SEQRES 29 A 614 ASP GLY GLY VAL TYR TRP GLU GLY ILE ASP GLU PRO LEU SEQRES 30 A 614 ALA PRO GLY VAL THR ILE THR SER TRP LYS ASN LYS GLU SEQRES 31 A 614 TRP ARG PRO GLN ASP GLU GLU PRO CYS ALA HIS PRO ASN SEQRES 32 A 614 SER ARG PHE CYS THR PRO ALA SER GLN CYS PRO ILE ILE SEQRES 33 A 614 ASP PRO ALA TRP GLU SER PRO GLU GLY VAL PRO ILE GLU SEQRES 34 A 614 GLY ILE ILE PHE GLY GLY ARG ARG PRO ALA GLY VAL PRO SEQRES 35 A 614 LEU VAL TYR GLU ALA LEU SER TRP GLN HIS GLY VAL PHE SEQRES 36 A 614 VAL GLY ALA ALA MET ARG SER GLU GLY GLY GLY ILE MET SEQRES 37 A 614 HIS ASP PRO PHE ALA MET ARG PRO PHE PHE GLY TYR ASN SEQRES 38 A 614 PHE GLY LYS TYR LEU ALA HIS TRP LEU SER MET ALA HIS SEQRES 39 A 614 ARG PRO ALA ALA LYS LEU PRO LYS ILE PHE HIS VAL ASN SEQRES 40 A 614 TRP PHE ARG LYS ASP LYS ASN GLY LYS PHE LEU TRP PRO SEQRES 41 A 614 GLY PHE GLY GLU ASN SER ARG VAL LEU GLU TRP MET PHE SEQRES 42 A 614 GLY ARG ILE GLU GLY GLU ASP SER ALA LYS LEU THR PRO SEQRES 43 A 614 ILE GLY TYR VAL PRO LYS GLU ASP ALA LEU ASN LEU LYS SEQRES 44 A 614 GLY LEU GLY ASP VAL ASN VAL GLU GLU LEU PHE GLY ILE SEQRES 45 A 614 SER LYS GLU PHE TRP GLU LYS GLU VAL GLU GLU ILE ASP SEQRES 46 A 614 LYS TYR LEU GLU ASP GLN VAL ASN ALA ASP LEU PRO TYR SEQRES 47 A 614 GLU ILE GLU ARG GLU LEU ARG ALA LEU LYS GLN ARG ILE SEQRES 48 A 614 SER GLN MET HET GTP A 701 32 HET MN A 702 1 HET MN A 703 1 HET NA A 704 1 HET OXL A 705 6 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM OXL OXALATE ION FORMUL 2 GTP C10 H16 N5 O14 P3 FORMUL 3 MN 2(MN 2+) FORMUL 5 NA NA 1+ FORMUL 6 OXL C2 O4 2- FORMUL 7 HOH *697(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 GLY A 579 1 7 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 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 LEU A 69 0 SHEET 2 C 5 CYS A 75 ALA A 78 -1 O CYS A 75 N LEU A 69 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 ALA A 313 N GLU A 263 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 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 ALA A 313 N GLU A 263 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 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 ILE A 475 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 704 1555 1555 2.24 LINK O ASN A 208 NA NA A 704 1555 1555 2.32 LINK NZ ALYS A 244 MN MN A 702 1555 1555 2.21 LINK NE2 HIS A 264 MN MN A 702 1555 1555 2.26 LINK OG1BTHR A 291 MN MN A 703 1555 1555 2.19 LINK OD1 ASP A 311 MN MN A 702 1555 1555 2.13 LINK O1G GTP A 701 MN MN A 702 1555 1555 2.19 LINK O2G GTP A 701 MN MN A 703 1555 1555 2.10 LINK O2B GTP A 701 MN MN A 703 1555 1555 2.18 LINK MN MN A 702 O2 OXL A 705 1555 1555 2.16 LINK MN MN A 702 O1 OXL A 705 1555 1555 2.16 LINK MN MN A 702 O HOH A1477 1555 1555 2.60 LINK MN MN A 703 O HOH A 821 1555 1555 2.22 LINK MN MN A 703 O HOH A 850 1555 1555 2.25 LINK MN MN A 703 O HOH A 855 1555 1555 2.25 LINK NA NA A 704 O HOH A 955 1555 1555 2.35 LINK NA NA A 704 O HOH A 983 1555 1555 2.34 LINK NA NA A 704 O HOH A1086 1555 1555 2.45 CISPEP 1 LEU A 200 PRO A 201 0 1.10 SITE 1 AC1 34 HIS A 264 PRO A 285 SER A 286 ALA A 287 SITE 2 AC1 34 CYS A 288 GLY A 289 LYS A 290 THR A 291 SITE 3 AC1 34 ASN A 292 ASP A 311 VAL A 335 ARG A 405 SITE 4 AC1 34 ARG A 436 TRP A 516 PHE A 517 PHE A 525 SITE 5 AC1 34 GLY A 529 PHE A 530 ASN A 533 MN A 702 SITE 6 AC1 34 MN A 703 OXL A 705 HOH A 816 HOH A 830 SITE 7 AC1 34 HOH A 836 HOH A 850 HOH A 855 HOH A 905 SITE 8 AC1 34 HOH A 921 HOH A1014 HOH A1094 HOH A1120 SITE 9 AC1 34 HOH A1218 HOH A1232 SITE 1 AC2 6 LYS A 244 HIS A 264 ASP A 311 GTP A 701 SITE 2 AC2 6 OXL A 705 HOH A1477 SITE 1 AC3 5 THR A 291 GTP A 701 HOH A 821 HOH A 850 SITE 2 AC3 5 HOH A 855 SITE 1 AC4 5 LEU A 79 ASN A 208 HOH A 955 HOH A 983 SITE 2 AC4 5 HOH A1086 SITE 1 AC5 11 ARG A 87 LYS A 244 HIS A 264 SER A 286 SITE 2 AC5 11 ASP A 311 ARG A 405 GTP A 701 MN A 702 SITE 3 AC5 11 HOH A 866 HOH A1059 HOH A1497 CRYST1 60.487 84.329 118.971 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 0.016532 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008405 0.00000