HEADER LYASE 14-JUL-08 3DT2 TITLE THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH OXALATE AND GTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC [GTP]; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPCK-C, PHOSPHOENOLPYRUVATE CARBOXYLASE; COMPND 5 EC: 4.1.1.32; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: PCK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T2 KEYWDS KINASE, GLUCONEOGENESIS, LYASE, DECARBOXYLASE, GTP-BINDING, KEYWDS 2 NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.M.SULLIVAN,T.HOLYOAK REVDAT 6 21-FEB-24 3DT2 1 REMARK SEQADV LINK REVDAT 5 25-OCT-17 3DT2 1 REMARK REVDAT 4 13-JUL-11 3DT2 1 VERSN REVDAT 3 24-FEB-09 3DT2 1 VERSN REVDAT 2 07-OCT-08 3DT2 1 JRNL REVDAT 1 26-AUG-08 3DT2 0 JRNL AUTH S.M.SULLIVAN,T.HOLYOAK JRNL TITL ENZYMES WITH LID-GATED ACTIVE SITES MUST OPERATE BY AN JRNL TITL 2 INDUCED FIT MECHANISM INSTEAD OF CONFORMATIONAL SELECTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 13829 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18772387 JRNL DOI 10.1073/PNAS.0805364105 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 98782 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4936 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6781 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 366 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4876 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 848 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : 0.01000 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): 0.071 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.092 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5350 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7295 ; 1.396 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 692 ; 5.900 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 247 ;34.221 ;24.372 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 938 ;13.708 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;16.079 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 758 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4150 ; 0.007 ; 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): 3236 ; 0.676 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5247 ; 1.194 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2114 ; 1.885 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2016 ; 3.064 ; 4.500 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 : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 358 REMARK 3 ORIGIN FOR THE GROUP (A): 15.6923 2.3775 17.4957 REMARK 3 T TENSOR REMARK 3 T11: 0.0234 T22: 0.0125 REMARK 3 T33: 0.0208 T12: -0.0036 REMARK 3 T13: -0.0018 T23: 0.0041 REMARK 3 L TENSOR REMARK 3 L11: 0.4457 L22: 0.2545 REMARK 3 L33: 0.3620 L12: -0.0326 REMARK 3 L13: -0.1636 L23: -0.0396 REMARK 3 S TENSOR REMARK 3 S11: 0.0116 S12: 0.0077 S13: 0.0117 REMARK 3 S21: -0.0210 S22: -0.0092 S23: -0.0350 REMARK 3 S31: -0.0157 S32: 0.0428 S33: -0.0023 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 359 A 405 REMARK 3 ORIGIN FOR THE GROUP (A): -6.3384 -6.9673 4.2625 REMARK 3 T TENSOR REMARK 3 T11: 0.0307 T22: 0.0360 REMARK 3 T33: 0.0035 T12: -0.0114 REMARK 3 T13: -0.0358 T23: -0.0159 REMARK 3 L TENSOR REMARK 3 L11: 1.4601 L22: 1.2979 REMARK 3 L33: 2.0454 L12: -0.7565 REMARK 3 L13: 0.8339 L23: -0.0862 REMARK 3 S TENSOR REMARK 3 S11: 0.1755 S12: 0.1543 S13: -0.2634 REMARK 3 S21: -0.2347 S22: -0.0823 S23: 0.1903 REMARK 3 S31: 0.2193 S32: -0.1835 S33: -0.0933 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 406 A 500 REMARK 3 ORIGIN FOR THE GROUP (A): 3.7940 -0.6412 33.0822 REMARK 3 T TENSOR REMARK 3 T11: 0.0170 T22: 0.0069 REMARK 3 T33: 0.0134 T12: -0.0030 REMARK 3 T13: -0.0071 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.3027 L22: 0.2441 REMARK 3 L33: 0.4787 L12: -0.0282 REMARK 3 L13: -0.0805 L23: -0.2397 REMARK 3 S TENSOR REMARK 3 S11: 0.0069 S12: 0.0038 S13: -0.0023 REMARK 3 S21: -0.0133 S22: -0.0098 S23: -0.0044 REMARK 3 S31: 0.0107 S32: 0.0139 S33: 0.0029 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 501 A 579 REMARK 3 ORIGIN FOR THE GROUP (A): -11.4007 1.2281 38.4007 REMARK 3 T TENSOR REMARK 3 T11: 0.0225 T22: 0.0128 REMARK 3 T33: 0.0299 T12: 0.0013 REMARK 3 T13: 0.0088 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.6735 L22: 1.2600 REMARK 3 L33: 1.4032 L12: -0.0932 REMARK 3 L13: 0.1416 L23: 0.0847 REMARK 3 S TENSOR REMARK 3 S11: 0.0205 S12: -0.0408 S13: -0.0147 REMARK 3 S21: 0.0524 S22: 0.0376 S23: 0.0952 REMARK 3 S31: -0.0323 S32: -0.0925 S33: -0.0581 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 580 A 622 REMARK 3 ORIGIN FOR THE GROUP (A): 1.5137 -13.5818 47.7011 REMARK 3 T TENSOR REMARK 3 T11: 0.0444 T22: 0.0035 REMARK 3 T33: 0.0096 T12: 0.0012 REMARK 3 T13: -0.0026 T23: 0.0131 REMARK 3 L TENSOR REMARK 3 L11: 1.4805 L22: 0.3618 REMARK 3 L33: 0.8711 L12: 0.2844 REMARK 3 L13: -0.2048 L23: -0.0518 REMARK 3 S TENSOR REMARK 3 S11: 0.0155 S12: -0.0959 S13: -0.0428 REMARK 3 S21: 0.0699 S22: -0.0247 S23: -0.0032 REMARK 3 S31: 0.0517 S32: 0.0287 S33: 0.0092 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3DT2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048452. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-07 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 : APS REMARK 200 BEAMLINE : 14-BM-C 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 : BENT GE(111) MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 98885 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.69000 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12-30% PEG 3350, 0.1M HEPES, 10 MM REMARK 280 MNCL2, PH 7.4, HANGING DROP VAPOR DIFFUSION, 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 30.21150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.51350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.45300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.51350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.21150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.45300 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1299 O HOH A 1733 1.83 REMARK 500 O HOH A 1317 O HOH A 1515 2.13 REMARK 500 NE ARG A 613 O HOH A 1560 2.17 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 OH TYR A 42 O HOH A 1813 2554 1.91 REMARK 500 OE2 GLU A 41 O HOH A 1938 2554 2.10 REMARK 500 NZ LYS A 594 O HOH A 1926 3545 2.11 REMARK 500 O HOH A 1204 O HOH A 1817 3555 2.12 REMARK 500 O HOH A 1138 O HOH A 1817 3555 2.14 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 -106.64 -135.64 REMARK 500 GLN A 110 92.72 82.44 REMARK 500 ARG A 129 -57.30 -123.31 REMARK 500 LYS A 243 -92.05 -83.41 REMARK 500 TRP A 260 -167.28 -119.02 REMARK 500 ASP A 311 -41.39 -142.85 REMARK 500 ASN A 344 68.64 -154.22 REMARK 500 ALA A 468 -152.67 -136.42 REMARK 500 LYS A 473 43.00 -108.88 REMARK 500 PHE A 480 16.30 57.57 REMARK 500 ALA A 505 -3.49 78.68 REMARK 500 PHE A 530 -130.17 50.96 REMARK 500 ASN A 601 -113.79 43.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1PE A 1100 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 A1000 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 79 O REMARK 620 2 ASN A 208 O 103.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 700 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 291 OG1 REMARK 620 2 GTP A 900 O1G 168.2 REMARK 620 3 GTP A 900 O1B 84.2 96.2 REMARK 620 4 HOH A1179 O 92.8 75.4 87.1 REMARK 620 5 HOH A1194 O 84.0 96.0 167.8 96.5 REMARK 620 6 HOH A1242 O 101.0 90.8 88.4 164.9 90.9 REMARK 620 N 1 2 3 4 5 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 ASP A 311 OD1 REMARK 620 2 OXL A 800 O2 170.2 REMARK 620 3 OXL A 800 O1 95.7 74.6 REMARK 620 4 GTP A 900 O3G 90.9 90.0 91.6 REMARK 620 N 1 2 3 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 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXL A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE A 1100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DT4 RELATED DB: PDB REMARK 900 COMPLEX WITH OXALATE AND GTP, OXALATE SOAKED INTO PEPCK-GTP REMARK 900 RELATED ID: 3DT7 RELATED DB: PDB REMARK 900 COMPLEX WITH SULFOPYRUVATE AND GTP REMARK 900 RELATED ID: 3DTB RELATED DB: PDB REMARK 900 COMPLEX WITH PHOSPHOGLYCOLATE AND GTP DBREF 3DT2 A 1 622 UNP P07379 PPCKC_RAT 1 622 SEQADV 3DT2 GLY A -1 UNP P07379 EXPRESSION TAG SEQADV 3DT2 SER A 0 UNP P07379 EXPRESSION TAG SEQRES 1 A 624 GLY SER MET PRO PRO GLN LEU HIS ASN GLY LEU ASP PHE SEQRES 2 A 624 SER ALA LYS VAL ILE GLN GLY SER LEU ASP SER LEU PRO SEQRES 3 A 624 GLN GLU VAL ARG LYS PHE VAL GLU GLY ASN ALA GLN LEU SEQRES 4 A 624 CYS GLN PRO GLU TYR ILE HIS ILE CYS ASP GLY SER GLU SEQRES 5 A 624 GLU GLU TYR GLY ARG LEU LEU ALA HIS MET GLN GLU GLU SEQRES 6 A 624 GLY VAL ILE ARG LYS LEU LYS LYS TYR ASP ASN CYS TRP SEQRES 7 A 624 LEU ALA LEU THR ASP PRO ARG ASP VAL ALA ARG ILE GLU SEQRES 8 A 624 SER LYS THR VAL ILE ILE THR GLN GLU GLN ARG ASP THR SEQRES 9 A 624 VAL PRO ILE PRO LYS SER GLY GLN SER GLN LEU GLY ARG SEQRES 10 A 624 TRP MET SER GLU GLU ASP PHE GLU LYS ALA PHE ASN ALA SEQRES 11 A 624 ARG PHE PRO GLY CYS MET LYS GLY ARG THR MET TYR VAL SEQRES 12 A 624 ILE PRO PHE SER MET GLY PRO LEU GLY SER PRO LEU ALA SEQRES 13 A 624 LYS ILE GLY ILE GLU LEU THR ASP SER PRO TYR VAL VAL SEQRES 14 A 624 ALA SER MET ARG ILE MET THR ARG MET GLY THR SER VAL SEQRES 15 A 624 LEU GLU ALA LEU GLY ASP GLY GLU PHE ILE LYS CYS LEU SEQRES 16 A 624 HIS SER VAL GLY CYS PRO LEU PRO LEU LYS LYS PRO LEU SEQRES 17 A 624 VAL ASN ASN TRP ALA CYS ASN PRO GLU LEU THR LEU ILE SEQRES 18 A 624 ALA HIS LEU PRO ASP ARG ARG GLU ILE ILE SER PHE GLY SEQRES 19 A 624 SER GLY TYR GLY GLY ASN SER LEU LEU GLY LYS LYS CYS SEQRES 20 A 624 PHE ALA LEU ARG ILE ALA SER ARG LEU ALA LYS GLU GLU SEQRES 21 A 624 GLY TRP LEU ALA GLU HIS MET LEU ILE LEU GLY ILE THR SEQRES 22 A 624 ASN PRO GLU GLY LYS LYS LYS TYR LEU ALA ALA ALA PHE SEQRES 23 A 624 PRO SER ALA CYS GLY LYS THR ASN LEU ALA MET MET ASN SEQRES 24 A 624 PRO THR LEU PRO GLY TRP LYS VAL GLU CYS VAL GLY ASP SEQRES 25 A 624 ASP ILE ALA TRP MET LYS PHE ASP ALA GLN GLY ASN LEU SEQRES 26 A 624 ARG ALA ILE ASN PRO GLU ASN GLY PHE PHE GLY VAL ALA SEQRES 27 A 624 PRO GLY THR SER VAL LYS THR ASN PRO ASN ALA ILE LYS SEQRES 28 A 624 THR ILE GLN LYS ASN THR ILE PHE THR ASN VAL ALA GLU SEQRES 29 A 624 THR SER ASP GLY GLY VAL TYR TRP GLU GLY ILE ASP GLU SEQRES 30 A 624 PRO LEU ALA PRO GLY VAL THR ILE THR SER TRP LYS ASN SEQRES 31 A 624 LYS GLU TRP ARG PRO GLN ASP GLU GLU PRO CYS ALA HIS SEQRES 32 A 624 PRO ASN SER ARG PHE CYS THR PRO ALA SER GLN CYS PRO SEQRES 33 A 624 ILE ILE ASP PRO ALA TRP GLU SER PRO GLU GLY VAL PRO SEQRES 34 A 624 ILE GLU GLY ILE ILE PHE GLY GLY ARG ARG PRO ALA GLY SEQRES 35 A 624 VAL PRO LEU VAL TYR GLU ALA LEU SER TRP GLN HIS GLY SEQRES 36 A 624 VAL PHE VAL GLY ALA ALA MET ARG SER GLU ALA THR ALA SEQRES 37 A 624 ALA ALA GLU HIS LYS GLY LYS VAL ILE MET HIS ASP PRO SEQRES 38 A 624 PHE ALA MET ARG PRO PHE PHE GLY TYR ASN PHE GLY LYS SEQRES 39 A 624 TYR LEU ALA HIS TRP LEU SER MET ALA HIS ARG PRO ALA SEQRES 40 A 624 ALA LYS LEU PRO LYS ILE PHE HIS VAL ASN TRP PHE ARG SEQRES 41 A 624 LYS ASP LYS ASN GLY LYS PHE LEU TRP PRO GLY PHE GLY SEQRES 42 A 624 GLU ASN SER ARG VAL LEU GLU TRP MET PHE GLY ARG ILE SEQRES 43 A 624 GLU GLY GLU ASP SER ALA LYS LEU THR PRO ILE GLY TYR SEQRES 44 A 624 VAL PRO LYS GLU ASP ALA LEU ASN LEU LYS GLY LEU GLY SEQRES 45 A 624 ASP VAL ASN VAL GLU GLU LEU PHE GLY ILE SER LYS GLU SEQRES 46 A 624 PHE TRP GLU LYS GLU VAL GLU GLU ILE ASP LYS TYR LEU SEQRES 47 A 624 GLU ASP GLN VAL ASN ALA ASP LEU PRO TYR GLU ILE GLU SEQRES 48 A 624 ARG GLU LEU ARG ALA LEU LYS GLN ARG ILE SER GLN MET HET MN A 700 1 HET MN A 701 1 HET OXL A 800 6 HET NA A1000 1 HET GTP A 900 32 HET 1PE A1100 10 HETNAM MN MANGANESE (II) ION HETNAM OXL OXALATE ION HETNAM NA SODIUM ION HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 2 MN 2(MN 2+) FORMUL 4 OXL C2 O4 2- FORMUL 5 NA NA 1+ FORMUL 6 GTP C10 H16 N5 O14 P3 FORMUL 7 1PE C10 H22 O6 FORMUL 8 HOH *848(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 LYS A 243 LEU A 248 1 6 HELIX 14 14 LEU A 248 GLY A 259 1 12 HELIX 15 15 GLY A 289 MET A 295 1 7 HELIX 16 16 ASN A 344 ILE A 351 1 8 HELIX 17 17 SER A 411 CYS A 413 5 3 HELIX 18 18 SER A 449 ALA A 459 1 11 HELIX 19 19 PRO A 479 MET A 482 5 4 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 LEU A 69 0 SHEET 2 C 5 CYS A 75 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 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 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 434 -1 O ILE A 428 N LEU A 323 SHEET 5 E 6 LYS A 510 VAL A 514 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 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 A1000 1555 1555 2.32 LINK O ASN A 208 NA NA A1000 1555 1555 2.28 LINK OG1 THR A 291 MN MN A 700 1555 1555 2.28 LINK OD1 ASP A 311 MN MN A 701 1555 1555 2.20 LINK MN MN A 700 O1G GTP A 900 1555 1555 2.17 LINK MN MN A 700 O1B GTP A 900 1555 1555 2.17 LINK MN MN A 700 O HOH A1179 1555 1555 2.25 LINK MN MN A 700 O HOH A1194 1555 1555 2.19 LINK MN MN A 700 O HOH A1242 1555 1555 2.15 LINK MN MN A 701 O2 OXL A 800 1555 1555 2.18 LINK MN MN A 701 O1 OXL A 800 1555 1555 2.20 LINK MN MN A 701 O3G GTP A 900 1555 1555 2.19 CISPEP 1 LEU A 200 PRO A 201 0 -3.60 SITE 1 AC1 4 THR A 291 HOH A1179 HOH A1194 HOH A1242 SITE 1 AC2 3 LYS A 244 HIS A 264 ASP A 311 SITE 1 AC3 10 ARG A 87 LYS A 244 HIS A 264 SER A 286 SITE 2 AC3 10 ASP A 311 ARG A 405 ALA A 467 HOH A1140 SITE 3 AC3 10 HOH A1168 HOH A1198 SITE 1 AC4 5 LEU A 79 ASN A 208 HOH A1217 HOH A1261 SITE 2 AC4 5 HOH A1422 SITE 1 AC5 29 HIS A 264 PRO A 285 SER A 286 ALA A 287 SITE 2 AC5 29 CYS A 288 GLY A 289 LYS A 290 THR A 291 SITE 3 AC5 29 ASN A 292 ASP A 311 PRO A 337 ARG A 405 SITE 4 AC5 29 ARG A 436 TRP A 516 PHE A 517 PHE A 525 SITE 5 AC5 29 GLY A 529 PHE A 530 ASN A 533 HOH A1114 SITE 6 AC5 29 HOH A1128 HOH A1172 HOH A1174 HOH A1179 SITE 7 AC5 29 HOH A1186 HOH A1197 HOH A1227 HOH A1242 SITE 8 AC5 29 HOH A1350 SITE 1 AC6 9 LEU A 153 TRP A 260 TRP A 314 MET A 315 SITE 2 AC6 9 LYS A 316 ARG A 324 GLU A 424 HOH A1477 SITE 3 AC6 9 HOH A1513 CRYST1 60.423 84.906 119.027 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 0.016550 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011778 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008401 0.00000