HEADER LYASE 20-MAR-15 4YW9 TITLE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH 3-MERCAPTOPICOLINIC TITLE 2 ACID AND GTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC [GTP]; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPCK-C; 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: 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: PGEX4T2 KEYWDS KINASE, GLUCONEOGENESIS, LYASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.D.BALAN,T.A.JOHNSON,M.J.MCLEOD,W.R.LOTOSKY,T.HOLYOAK REVDAT 6 27-SEP-23 4YW9 1 LINK REVDAT 5 04-DEC-19 4YW9 1 REMARK REVDAT 4 20-SEP-17 4YW9 1 JRNL REMARK REVDAT 3 08-JUN-16 4YW9 1 JRNL REVDAT 2 28-OCT-15 4YW9 1 JRNL REVDAT 1 23-SEP-15 4YW9 0 JRNL AUTH M.D.BALAN,M.J.MCLEOD,W.R.LOTOSKY,M.GHALY,T.HOLYOAK JRNL TITL INHIBITION AND ALLOSTERIC REGULATION OF MONOMERIC JRNL TITL 2 PHOSPHOENOLPYRUVATE CARBOXYKINASE BY 3-MERCAPTOPICOLINIC JRNL TITL 3 ACID. JRNL REF BIOCHEMISTRY V. 54 5878 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 26322521 JRNL DOI 10.1021/ACS.BIOCHEM.5B00822 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 29.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 104796 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 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 : 5550 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) : 1.42 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5171 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.3800 REMARK 3 BIN FREE R VALUE SET COUNT : 293 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4818 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 684 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.064 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.296 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5203 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4981 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7082 ; 1.787 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11552 ; 0.839 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 667 ; 6.260 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 233 ;34.084 ;24.077 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 920 ;13.305 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;16.283 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 739 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5881 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1178 ; 0.001 ; 0.020 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4YW9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208191. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-09 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) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SIDE SCATTERING BENT CUBE-ROOT I REMARK 200 -BEAM SINGLE CRYSTAL REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 110377 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 (%) : 94.4 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 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 (%) : 76.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.41700 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 2QEW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M HEPES PH 7.4,2 MM REMARK 280 MNCL2, 10MM GTP, 1MM 3-MERCAPTOPICOLINIC ACID, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 59.37100 REMARK 290 SMTRY3 2 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 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 GLN A 394 REMARK 465 ASP A 395 REMARK 465 GLU A 396 REMARK 465 THR A 465 REMARK 465 ALA A 466 REMARK 465 ALA A 467 REMARK 465 ALA A 468 REMARK 465 GLU A 469 REMARK 465 HIS A 470 REMARK 465 LYS A 471 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 ND1 HIS A 477 O HOH A 804 1.86 REMARK 500 OE1 GLU A 375 O HOH A 805 1.90 REMARK 500 NE2 GLN A 110 O HOH A 806 1.93 REMARK 500 OH TYR A 42 O HOH A 807 1.95 REMARK 500 NE ARG A 483 O HOH A 808 2.03 REMARK 500 O HOH A 1074 O HOH A 1231 2.09 REMARK 500 NZ LYS A 276 O HOH A 809 2.10 REMARK 500 NZ LYS A 256 O HOH A 810 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 ASP A 47 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 PHE A 246 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ASP A 311 OD1 - CG - OD2 ANGL. DEV. = -15.7 DEGREES REMARK 500 ASP A 311 CB - CG - OD1 ANGL. DEV. = 16.7 DEGREES REMARK 500 ARG A 461 NE - CZ - NH2 ANGL. DEV. = -3.2 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 -131.22 -128.48 REMARK 500 ARG A 129 -58.39 -125.06 REMARK 500 LYS A 244 -45.92 -132.75 REMARK 500 TRP A 260 -169.11 -126.69 REMARK 500 ASP A 311 -34.99 -150.48 REMARK 500 ASN A 344 71.00 -165.28 REMARK 500 PHE A 480 15.79 57.44 REMARK 500 ALA A 505 -23.35 90.92 REMARK 500 PHE A 530 -121.63 49.63 REMARK 500 LYS A 560 158.17 -47.90 REMARK 500 ASP A 562 -4.48 75.77 REMARK 500 ASN A 601 -118.37 52.85 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 708 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 MN A 703 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 63 OE1 REMARK 620 2 GLU A 63 OE2 52.1 REMARK 620 3 HIS A 502 NE2 28.4 77.2 REMARK 620 4 GLU A 607 OE1 25.3 75.6 4.5 REMARK 620 5 GLU A 607 OE2 25.4 75.6 4.1 0.5 REMARK 620 6 HOH A 980 O 25.5 74.8 2.9 2.6 2.1 REMARK 620 N 1 2 3 4 5 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 101.5 REMARK 620 3 HOH A 959 O 98.5 159.1 REMARK 620 4 HOH A1209 O 97.1 92.3 91.1 REMARK 620 5 HOH A1306 O 109.3 82.2 85.7 153.6 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 81.9 REMARK 620 3 ASP A 311 OD1 91.6 91.9 REMARK 620 4 GTP A 701 O1G 172.7 94.7 95.1 REMARK 620 5 1WD A 706 N4 88.4 165.9 98.7 93.6 REMARK 620 6 1WD A 706 O10 88.7 95.9 172.2 85.1 73.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 705 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 291 OG1 REMARK 620 2 GTP A 701 O3G 178.4 REMARK 620 3 GTP A 701 O1B 88.8 92.2 REMARK 620 4 HOH A 859 O 86.2 92.7 87.9 REMARK 620 5 HOH A 890 O 83.9 95.2 170.7 97.3 REMARK 620 6 HOH A1044 O 92.2 89.0 87.2 174.9 87.3 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 MN A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1WD A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 708 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YW8 RELATED DB: PDB DBREF 4YW9 A 1 622 UNP P07379 PCKGC_RAT 1 622 SEQADV 4YW9 GLY A -1 UNP P07379 EXPRESSION TAG SEQADV 4YW9 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 GTP A 701 32 HET MN A 702 1 HET MN A 703 1 HET NA A 704 1 HET MN A 705 1 HET 1WD A 706 10 HET MOH A 707 2 HET 1PE A 708 7 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM 1WD 3-SULFANYLPYRIDINE-2-CARBOXYLIC ACID HETNAM MOH METHANOL HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 2 GTP C10 H16 N5 O14 P3 FORMUL 3 MN 3(MN 2+) FORMUL 5 NA NA 1+ FORMUL 7 1WD C6 H5 N O2 S FORMUL 8 MOH C H4 O FORMUL 9 1PE C10 H22 O6 FORMUL 10 HOH *684(H2 O) HELIX 1 AA1 PHE A 11 ALA A 13 5 3 HELIX 2 AA2 SER A 19 LEU A 23 5 5 HELIX 3 AA3 PRO A 24 GLN A 39 1 16 HELIX 4 AA4 SER A 49 GLU A 63 1 15 HELIX 5 AA5 ILE A 88 SER A 90 5 3 HELIX 6 AA6 GLU A 98 VAL A 103 1 6 HELIX 7 AA7 SER A 118 ALA A 128 1 11 HELIX 8 AA8 SER A 163 THR A 174 1 12 HELIX 9 AA9 GLY A 177 GLY A 185 1 9 HELIX 10 AB1 ASN A 213 THR A 217 5 5 HELIX 11 AB2 PRO A 223 ARG A 225 5 3 HELIX 12 AB3 TYR A 235 LEU A 240 1 6 HELIX 13 AB4 LEU A 248 GLY A 259 1 12 HELIX 14 AB5 GLY A 289 MET A 295 1 7 HELIX 15 AB6 ASN A 344 ILE A 351 1 8 HELIX 16 AB7 SER A 411 CYS A 413 5 3 HELIX 17 AB8 SER A 449 ALA A 459 1 11 HELIX 18 AB9 PRO A 479 MET A 482 5 4 HELIX 19 AC1 ASN A 489 MET A 500 1 12 HELIX 20 AC2 ALA A 501 ARG A 503 5 3 HELIX 21 AC3 GLY A 529 GLU A 532 5 4 HELIX 22 AC4 ASN A 533 GLU A 545 1 13 HELIX 23 AC5 ASN A 573 GLY A 579 1 7 HELIX 24 AC6 SER A 581 VAL A 600 1 20 HELIX 25 AC7 ASN A 601 LEU A 604 5 4 HELIX 26 AC8 PRO A 605 GLN A 621 1 17 SHEET 1 AA1 9 VAL A 15 GLN A 17 0 SHEET 2 AA1 9 TYR A 42 ILE A 45 1 O ILE A 43 N ILE A 16 SHEET 3 AA1 9 THR A 138 MET A 146 1 O MET A 139 N TYR A 42 SHEET 4 AA1 9 LYS A 155 THR A 161 -1 O THR A 161 N TYR A 140 SHEET 5 AA1 9 ILE A 190 SER A 195 1 O CYS A 192 N LEU A 160 SHEET 6 AA1 9 GLU A 227 PHE A 231 1 O SER A 230 N LEU A 193 SHEET 7 AA1 9 LEU A 218 LEU A 222 -1 N LEU A 222 O GLU A 227 SHEET 8 AA1 9 THR A 92 ILE A 95 1 N ILE A 95 O HIS A 221 SHEET 9 AA1 9 TRP A 116 MET A 117 1 O MET A 117 N ILE A 94 SHEET 1 AA2 4 VAL A 15 GLN A 17 0 SHEET 2 AA2 4 TYR A 42 ILE A 45 1 O ILE A 43 N ILE A 16 SHEET 3 AA2 4 THR A 138 MET A 146 1 O MET A 139 N TYR A 42 SHEET 4 AA2 4 ARG A 175 MET A 176 -1 O ARG A 175 N SER A 145 SHEET 1 AA3 5 ARG A 67 LYS A 68 0 SHEET 2 AA3 5 TRP A 76 ALA A 78 -1 O LEU A 77 N ARG A 67 SHEET 3 AA3 5 ILE A 356 THR A 358 1 O PHE A 357 N TRP A 76 SHEET 4 AA3 5 ARG A 405 PRO A 409 -1 O ARG A 405 N THR A 358 SHEET 5 AA3 5 GLY A 331 VAL A 335 -1 N GLY A 334 O PHE A 406 SHEET 1 AA4 7 LEU A 261 GLU A 263 0 SHEET 2 AA4 7 ALA A 313 PHE A 317 -1 O ALA A 313 N GLU A 263 SHEET 3 AA4 7 LEU A 323 ILE A 326 -1 O ILE A 326 N TRP A 314 SHEET 4 AA4 7 VAL A 426 GLY A 434 -1 O ILE A 428 N LEU A 323 SHEET 5 AA4 7 LYS A 277 ALA A 283 1 N TYR A 279 O GLU A 429 SHEET 6 AA4 7 LEU A 266 THR A 271 -1 N ILE A 270 O LYS A 278 SHEET 7 AA4 7 LYS A 304 GLY A 309 -1 O GLU A 306 N GLY A 269 SHEET 1 AA5 6 LEU A 261 GLU A 263 0 SHEET 2 AA5 6 ALA A 313 PHE A 317 -1 O ALA A 313 N GLU A 263 SHEET 3 AA5 6 LEU A 323 ILE A 326 -1 O ILE A 326 N TRP A 314 SHEET 4 AA5 6 VAL A 426 GLY A 434 -1 O ILE A 428 N LEU A 323 SHEET 5 AA5 6 LYS A 510 VAL A 514 1 O PHE A 512 N PHE A 433 SHEET 6 AA5 6 VAL A 444 GLU A 446 -1 N TYR A 445 O HIS A 513 SHEET 1 AA6 4 VAL A 368 TYR A 369 0 SHEET 2 AA6 4 ALA A 361 THR A 363 -1 N ALA A 361 O TYR A 369 SHEET 3 AA6 4 ILE A 383 THR A 384 -1 O THR A 384 N GLU A 362 SHEET 4 AA6 4 GLU A 390 TRP A 391 -1 O TRP A 391 N ILE A 383 SHEET 1 AA7 2 ARG A 461 GLU A 463 0 SHEET 2 AA7 2 ILE A 475 HIS A 477 -1 O MET A 476 N SER A 462 SHEET 1 AA8 2 ALA A 550 THR A 553 0 SHEET 2 AA8 2 GLY A 556 PRO A 559 -1 O VAL A 558 N LYS A 551 LINK OE1AGLU A 63 MN MN A 703 1555 2545 2.41 LINK OE2BGLU A 63 MN MN A 703 1555 2545 2.14 LINK O LEU A 79 NA NA A 704 1555 1555 2.35 LINK O ASN A 208 NA NA A 704 1555 1555 2.30 LINK NZ LYS A 244 MN MN A 702 1555 1555 2.29 LINK NE2 HIS A 264 MN MN A 702 1555 1555 2.31 LINK OG1 THR A 291 MN MN A 705 1555 1555 2.30 LINK OD1 ASP A 311 MN MN A 702 1555 1555 2.00 LINK NE2 HIS A 502 MN MN A 703 1555 1555 2.56 LINK OE1BGLU A 607 MN MN A 703 1555 1555 2.63 LINK OE2BGLU A 607 MN MN A 703 1555 1555 1.87 LINK O1G GTP A 701 MN MN A 702 1555 1555 2.11 LINK O3G GTP A 701 MN MN A 705 1555 1555 2.15 LINK O1B GTP A 701 MN MN A 705 1555 1555 2.19 LINK MN MN A 702 N4 1WD A 706 1555 1555 2.26 LINK MN MN A 702 O10 1WD A 706 1555 1555 2.11 LINK MN MN A 703 O HOH A 980 1555 1555 2.74 LINK NA NA A 704 O HOH A 959 1555 1555 2.37 LINK NA NA A 704 O HOH A1209 1555 1555 2.17 LINK NA NA A 704 O HOH A1306 1555 1555 2.49 LINK MN MN A 705 O HOH A 859 1555 1555 2.26 LINK MN MN A 705 O HOH A 890 1555 1555 2.26 LINK MN MN A 705 O HOH A1044 1555 1555 2.22 CISPEP 1 LEU A 200 PRO A 201 0 1.50 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 705 1WD A 706 HOH A 842 HOH A 859 SITE 7 AC1 34 HOH A 873 HOH A 878 HOH A 893 HOH A 902 SITE 8 AC1 34 HOH A 961 HOH A1030 HOH A1044 HOH A1083 SITE 9 AC1 34 HOH A1246 HOH A1275 SITE 1 AC2 5 LYS A 244 HIS A 264 ASP A 311 GTP A 701 SITE 2 AC2 5 1WD A 706 SITE 1 AC3 3 HIS A 502 GLU A 607 HOH A 980 SITE 1 AC4 5 LEU A 79 ASN A 208 HOH A 959 HOH A1209 SITE 2 AC4 5 HOH A1306 SITE 1 AC5 5 THR A 291 GTP A 701 HOH A 859 HOH A 890 SITE 2 AC5 5 HOH A1044 SITE 1 AC6 12 ARG A 87 TYR A 235 LYS A 243 LYS A 244 SITE 2 AC6 12 HIS A 264 SER A 286 ASP A 311 PHE A 333 SITE 3 AC6 12 ARG A 405 GTP A 701 MN A 702 HOH A 996 SITE 1 AC7 5 ASP A 10 PHE A 11 ALA A 13 LYS A 14 SITE 2 AC7 5 HOH A 921 CRYST1 44.407 118.742 60.248 90.00 110.02 90.00 P 1 21 1 2 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 0.022519 0.000000 0.008205 0.00000 SCALE2 0.000000 0.008422 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017666 0.00000