HEADER LYASE 20-MAR-15 4YWD TITLE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH 2,3-PYRIDINE TITLE 2 DICARBOXYLIC ACID 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: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS KINASE, GLUCONEOGENESIS, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR M.D.BALAN,T.A.JOHNSON,M.J.MCLEOD,W.R.LOTOSKY,T.HOLYOAK REVDAT 7 27-SEP-23 4YWD 1 LINK REVDAT 6 04-DEC-19 4YWD 1 REMARK REVDAT 5 20-SEP-17 4YWD 1 JRNL REMARK REVDAT 4 08-JUN-16 4YWD 1 JRNL REVDAT 3 01-JUN-16 4YWD 1 REMARK REVDAT 2 28-OCT-15 4YWD 1 JRNL REVDAT 1 23-SEP-15 4YWD 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 33269 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1678 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1538 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.57 REMARK 3 BIN R VALUE (WORKING SET) : 0.3290 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4754 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 232 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.08000 REMARK 3 B22 (A**2) : -0.67000 REMARK 3 B33 (A**2) : 1.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.60000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.282 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.206 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.160 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.932 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4912 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4663 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6655 ; 1.081 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10783 ; 0.705 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 608 ; 6.006 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 217 ;33.551 ;24.101 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 840 ;13.802 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;13.445 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 699 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5540 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1106 ; 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 : 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 9 A 285 REMARK 3 ORIGIN FOR THE GROUP (A): 0.8329 -8.2040 -3.1715 REMARK 3 T TENSOR REMARK 3 T11: 0.1297 T22: 0.1761 REMARK 3 T33: 0.0221 T12: -0.0120 REMARK 3 T13: -0.0424 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.9907 L22: 2.8208 REMARK 3 L33: 0.9956 L12: -0.1431 REMARK 3 L13: -0.3830 L23: 0.9194 REMARK 3 S TENSOR REMARK 3 S11: 0.0233 S12: 0.0802 S13: -0.0334 REMARK 3 S21: 0.0868 S22: -0.0766 S23: 0.0482 REMARK 3 S31: 0.1005 S32: -0.0049 S33: 0.0533 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 286 A 333 REMARK 3 ORIGIN FOR THE GROUP (A): -13.4674 3.4492 10.7630 REMARK 3 T TENSOR REMARK 3 T11: 0.2268 T22: 0.2497 REMARK 3 T33: 0.1408 T12: -0.0510 REMARK 3 T13: 0.0322 T23: -0.0606 REMARK 3 L TENSOR REMARK 3 L11: 1.6815 L22: 2.2302 REMARK 3 L33: 2.4641 L12: -0.0153 REMARK 3 L13: -1.6727 L23: 0.8487 REMARK 3 S TENSOR REMARK 3 S11: -0.1997 S12: -0.1597 S13: -0.1222 REMARK 3 S21: 0.4378 S22: -0.0964 S23: 0.1146 REMARK 3 S31: 0.2846 S32: -0.0639 S33: 0.2962 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 334 A 412 REMARK 3 ORIGIN FOR THE GROUP (A): -3.8090 -17.0812 19.9434 REMARK 3 T TENSOR REMARK 3 T11: 0.7177 T22: 0.2214 REMARK 3 T33: 0.0894 T12: -0.0983 REMARK 3 T13: 0.0860 T23: 0.0200 REMARK 3 L TENSOR REMARK 3 L11: 2.0466 L22: 3.5124 REMARK 3 L33: 3.9026 L12: -0.3699 REMARK 3 L13: 0.6969 L23: -0.5759 REMARK 3 S TENSOR REMARK 3 S11: 0.0365 S12: -0.4675 S13: -0.1903 REMARK 3 S21: 1.1316 S22: -0.0885 S23: 0.2115 REMARK 3 S31: 0.3404 S32: 0.0516 S33: 0.0520 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 413 A 544 REMARK 3 ORIGIN FOR THE GROUP (A): -5.3313 11.4048 15.8217 REMARK 3 T TENSOR REMARK 3 T11: 0.2436 T22: 0.1280 REMARK 3 T33: 0.0360 T12: 0.0036 REMARK 3 T13: 0.0046 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 2.5957 L22: 1.7761 REMARK 3 L33: 1.5850 L12: 0.6968 REMARK 3 L13: -1.1120 L23: 1.0003 REMARK 3 S TENSOR REMARK 3 S11: -0.0726 S12: -0.1693 S13: -0.1480 REMARK 3 S21: 0.3341 S22: -0.1337 S23: 0.1268 REMARK 3 S31: 0.2410 S32: -0.0358 S33: 0.2062 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 545 A 622 REMARK 3 ORIGIN FOR THE GROUP (A): -0.5159 21.4784 22.7008 REMARK 3 T TENSOR REMARK 3 T11: 0.3168 T22: 0.1867 REMARK 3 T33: 0.0426 T12: -0.0140 REMARK 3 T13: -0.0739 T23: -0.0084 REMARK 3 L TENSOR REMARK 3 L11: 2.0699 L22: 2.2081 REMARK 3 L33: 2.3493 L12: -0.1013 REMARK 3 L13: -0.1351 L23: 1.1640 REMARK 3 S TENSOR REMARK 3 S11: 0.0331 S12: -0.4751 S13: 0.0687 REMARK 3 S21: 0.4750 S22: -0.1264 S23: 0.0157 REMARK 3 S31: -0.0912 S32: 0.0345 S33: 0.0934 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 4 REMARK 4 4YWD 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_1000208194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000, DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33335 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 92.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.51900 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 (%): 45.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M HEPES PH 7.4,2 MM REMARK 280 MNCL2, 1MM 2,3-PYRIDINE DICARBOXYLIC 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 59.70250 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 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 GLN A 394 REMARK 465 ASP A 395 REMARK 465 GLU A 396 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: 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 ARG A 129 -52.72 -122.45 REMARK 500 LYS A 243 -91.31 -78.35 REMARK 500 TRP A 260 -169.60 -125.22 REMARK 500 ALA A 287 98.80 -60.14 REMARK 500 CYS A 288 -144.46 -69.09 REMARK 500 ASP A 311 -52.51 -142.94 REMARK 500 PHE A 333 70.42 -110.95 REMARK 500 ASN A 344 73.93 -158.60 REMARK 500 PHE A 480 16.20 58.27 REMARK 500 PHE A 530 -128.86 52.16 REMARK 500 ASP A 548 56.51 -96.34 REMARK 500 ASN A 601 -122.04 58.57 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 MN A 702 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 63 OE2 REMARK 620 2 HIS A 502 NE2 20.1 REMARK 620 3 GLU A 607 OE2 18.0 4.3 REMARK 620 4 HOH A 862 O 20.0 2.4 2.5 REMARK 620 5 HOH A 924 O 17.3 3.0 2.6 2.9 REMARK 620 6 HOH A 938 O 17.4 2.9 2.6 2.8 0.1 REMARK 620 N 1 2 3 4 5 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 96.1 REMARK 620 3 HOH A 847 O 102.4 88.1 REMARK 620 4 HOH A 944 O 93.9 169.9 91.3 REMARK 620 N 1 2 3 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 89.7 REMARK 620 3 ASP A 311 OD1 99.6 94.6 REMARK 620 4 NTM A 704 N1 98.5 159.8 102.1 REMARK 620 5 NTM A 704 O1 87.7 87.8 172.3 74.2 REMARK 620 6 HOH A 979 O 171.1 83.4 86.6 86.4 86.4 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 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 NTM A 704 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WY8 RELATED DB: PDB REMARK 900 RELATED ID: 4WY9 RELATED DB: PDB REMARK 900 RELATED ID: 4WYB RELATED DB: PDB DBREF 4YWD A 1 622 UNP P07379 PCKGC_RAT 1 622 SEQRES 1 A 622 MET PRO PRO GLN LEU HIS ASN GLY LEU ASP PHE SER ALA SEQRES 2 A 622 LYS VAL ILE GLN GLY SER LEU ASP SER LEU PRO GLN GLU SEQRES 3 A 622 VAL ARG LYS PHE VAL GLU GLY ASN ALA GLN LEU CYS GLN SEQRES 4 A 622 PRO GLU TYR ILE HIS ILE CYS ASP GLY SER GLU GLU GLU SEQRES 5 A 622 TYR GLY ARG LEU LEU ALA HIS MET GLN GLU GLU GLY VAL SEQRES 6 A 622 ILE ARG LYS LEU LYS LYS TYR ASP ASN CYS TRP LEU ALA SEQRES 7 A 622 LEU THR ASP PRO ARG ASP VAL ALA ARG ILE GLU SER LYS SEQRES 8 A 622 THR VAL ILE ILE THR GLN GLU GLN ARG ASP THR VAL PRO SEQRES 9 A 622 ILE PRO LYS SER GLY GLN SER GLN LEU GLY ARG TRP MET SEQRES 10 A 622 SER GLU GLU ASP PHE GLU LYS ALA PHE ASN ALA ARG PHE SEQRES 11 A 622 PRO GLY CYS MET LYS GLY ARG THR MET TYR VAL ILE PRO SEQRES 12 A 622 PHE SER MET GLY PRO LEU GLY SER PRO LEU ALA LYS ILE SEQRES 13 A 622 GLY ILE GLU LEU THR ASP SER PRO TYR VAL VAL ALA SER SEQRES 14 A 622 MET ARG ILE MET THR ARG MET GLY THR SER VAL LEU GLU SEQRES 15 A 622 ALA LEU GLY ASP GLY GLU PHE ILE LYS CYS LEU HIS SER SEQRES 16 A 622 VAL GLY CYS PRO LEU PRO LEU LYS LYS PRO LEU VAL ASN SEQRES 17 A 622 ASN TRP ALA CYS ASN PRO GLU LEU THR LEU ILE ALA HIS SEQRES 18 A 622 LEU PRO ASP ARG ARG GLU ILE ILE SER PHE GLY SER GLY SEQRES 19 A 622 TYR GLY GLY ASN SER LEU LEU GLY LYS LYS CYS PHE ALA SEQRES 20 A 622 LEU ARG ILE ALA SER ARG LEU ALA LYS GLU GLU GLY TRP SEQRES 21 A 622 LEU ALA GLU HIS MET LEU ILE LEU GLY ILE THR ASN PRO SEQRES 22 A 622 GLU GLY LYS LYS LYS TYR LEU ALA ALA ALA PHE PRO SER SEQRES 23 A 622 ALA CYS GLY LYS THR ASN LEU ALA MET MET ASN PRO THR SEQRES 24 A 622 LEU PRO GLY TRP LYS VAL GLU CYS VAL GLY ASP ASP ILE SEQRES 25 A 622 ALA TRP MET LYS PHE ASP ALA GLN GLY ASN LEU ARG ALA SEQRES 26 A 622 ILE ASN PRO GLU ASN GLY PHE PHE GLY VAL ALA PRO GLY SEQRES 27 A 622 THR SER VAL LYS THR ASN PRO ASN ALA ILE LYS THR ILE SEQRES 28 A 622 GLN LYS ASN THR ILE PHE THR ASN VAL ALA GLU THR SER SEQRES 29 A 622 ASP GLY GLY VAL TYR TRP GLU GLY ILE ASP GLU PRO LEU SEQRES 30 A 622 ALA PRO GLY VAL THR ILE THR SER TRP LYS ASN LYS GLU SEQRES 31 A 622 TRP ARG PRO GLN ASP GLU GLU PRO CYS ALA HIS PRO ASN SEQRES 32 A 622 SER ARG PHE CYS THR PRO ALA SER GLN CYS PRO ILE ILE SEQRES 33 A 622 ASP PRO ALA TRP GLU SER PRO GLU GLY VAL PRO ILE GLU SEQRES 34 A 622 GLY ILE ILE PHE GLY GLY ARG ARG PRO ALA GLY VAL PRO SEQRES 35 A 622 LEU VAL TYR GLU ALA LEU SER TRP GLN HIS GLY VAL PHE SEQRES 36 A 622 VAL GLY ALA ALA MET ARG SER GLU ALA THR ALA ALA ALA SEQRES 37 A 622 GLU HIS LYS GLY LYS VAL ILE MET HIS ASP PRO PHE ALA SEQRES 38 A 622 MET ARG PRO PHE PHE GLY TYR ASN PHE GLY LYS TYR LEU SEQRES 39 A 622 ALA HIS TRP LEU SER MET ALA HIS ARG PRO ALA ALA LYS SEQRES 40 A 622 LEU PRO LYS ILE PHE HIS VAL ASN TRP PHE ARG LYS ASP SEQRES 41 A 622 LYS ASN GLY LYS PHE LEU TRP PRO GLY PHE GLY GLU ASN SEQRES 42 A 622 SER ARG VAL LEU GLU TRP MET PHE GLY ARG ILE GLU GLY SEQRES 43 A 622 GLU ASP SER ALA LYS LEU THR PRO ILE GLY TYR VAL PRO SEQRES 44 A 622 LYS GLU ASP ALA LEU ASN LEU LYS GLY LEU GLY ASP VAL SEQRES 45 A 622 ASN VAL GLU GLU LEU PHE GLY ILE SER LYS GLU PHE TRP SEQRES 46 A 622 GLU LYS GLU VAL GLU GLU ILE ASP LYS TYR LEU GLU ASP SEQRES 47 A 622 GLN VAL ASN ALA ASP LEU PRO TYR GLU ILE GLU ARG GLU SEQRES 48 A 622 LEU ARG ALA LEU LYS GLN ARG ILE SER GLN MET HET MN A 701 1 HET MN A 702 1 HET NA A 703 1 HET NTM A 704 12 HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM NTM QUINOLINIC ACID FORMUL 2 MN 2(MN 2+) FORMUL 4 NA NA 1+ FORMUL 5 NTM C7 H5 N O4 FORMUL 6 HOH *232(H2 O) HELIX 1 AA1 PHE A 11 ALA A 13 5 3 HELIX 2 AA2 PRO A 24 GLN A 39 1 16 HELIX 3 AA3 SER A 49 GLU A 63 1 15 HELIX 4 AA4 ILE A 88 SER A 90 5 3 HELIX 5 AA5 GLU A 98 VAL A 103 1 6 HELIX 6 AA6 SER A 118 ALA A 128 1 11 HELIX 7 AA7 SER A 163 THR A 174 1 12 HELIX 8 AA8 GLY A 177 GLY A 185 1 9 HELIX 9 AA9 ASN A 213 THR A 217 5 5 HELIX 10 AB1 TYR A 235 LEU A 240 1 6 HELIX 11 AB2 LEU A 248 GLY A 259 1 12 HELIX 12 AB3 GLY A 289 MET A 295 1 7 HELIX 13 AB4 ASN A 344 ILE A 351 1 8 HELIX 14 AB5 SER A 411 CYS A 413 5 3 HELIX 15 AB6 SER A 449 ALA A 459 1 11 HELIX 16 AB7 PRO A 479 MET A 482 5 4 HELIX 17 AB8 ASN A 489 MET A 500 1 12 HELIX 18 AB9 ALA A 501 ARG A 503 5 3 HELIX 19 AC1 GLY A 529 GLU A 532 5 4 HELIX 20 AC2 ASN A 533 GLU A 545 1 13 HELIX 21 AC3 ASN A 573 PHE A 578 1 6 HELIX 22 AC4 SER A 581 VAL A 600 1 20 HELIX 23 AC5 ASN A 601 LEU A 604 5 4 HELIX 24 AC6 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 VAL A 141 N HIS A 44 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 ILE A 158 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 218 O PHE A 231 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 VAL A 141 N HIS A 44 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 PHE A 332 O THR A 408 SHEET 1 AA4 7 LEU A 261 GLU A 263 0 SHEET 2 AA4 7 ALA A 313 PHE A 317 -1 O MET A 315 N LEU A 261 SHEET 3 AA4 7 LEU A 323 ILE A 326 -1 O ARG A 324 N LYS A 316 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 ALA A 281 O ILE A 432 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 MET A 315 N LEU A 261 SHEET 3 AA5 6 LEU A 323 ILE A 326 -1 O ARG A 324 N LYS A 316 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 ILE A 431 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 OE2 GLU A 63 MN MN A 702 1555 2545 2.08 LINK O LEU A 79 NA NA A 703 1555 1555 2.43 LINK O ASN A 208 NA NA A 703 1555 1555 2.22 LINK NZ LYS A 244 MN MN A 701 1555 1555 2.44 LINK NE2 HIS A 264 MN MN A 701 1555 1555 2.31 LINK OD1 ASP A 311 MN MN A 701 1555 1555 2.06 LINK NE2 HIS A 502 MN MN A 702 1555 1555 2.43 LINK OE2 GLU A 607 MN MN A 702 1555 1555 2.23 LINK MN MN A 701 N1 NTM A 704 1555 1555 2.15 LINK MN MN A 701 O1 NTM A 704 1555 1555 2.10 LINK MN MN A 701 O HOH A 979 1555 1555 2.40 LINK MN MN A 702 O HOH A 862 1555 1555 2.06 LINK MN MN A 702 O HOH A 924 1555 1555 2.07 LINK MN MN A 702 O HOH A 938 1555 1555 2.55 LINK NA NA A 703 O HOH A 847 1555 1555 2.39 LINK NA NA A 703 O HOH A 944 1555 1555 2.02 CISPEP 1 LEU A 200 PRO A 201 0 -2.18 SITE 1 AC1 5 LYS A 244 HIS A 264 ASP A 311 NTM A 704 SITE 2 AC1 5 HOH A 979 SITE 1 AC2 5 HIS A 502 GLU A 607 HOH A 862 HOH A 924 SITE 2 AC2 5 HOH A 938 SITE 1 AC3 4 LEU A 79 ASN A 208 HOH A 847 HOH A 944 SITE 1 AC4 13 ARG A 87 TYR A 235 LYS A 243 LYS A 244 SITE 2 AC4 13 HIS A 264 SER A 286 ASP A 311 PHE A 333 SITE 3 AC4 13 ARG A 405 MN A 701 HOH A 801 HOH A 812 SITE 4 AC4 13 HOH A 979 CRYST1 45.340 119.405 61.015 90.00 109.16 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 0.022056 0.000000 0.007665 0.00000 SCALE2 0.000000 0.008375 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017351 0.00000