HEADER LYASE 15-MAY-07 2PY7 TITLE CRYSTAL STRUCTURE OF E. COLI PHOSPHOENOLPYRUVATE CARBOXYKINASE MUTANT TITLE 2 LYS213SER COMPLEXED WITH ATP-MG2+-MN2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOENOLPYRUVATE CARBOXYKINASE; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: PEP CARBOXYKINASE, PHOSPHOENOLPYRUVATE CARBOXYLASE, PEPCK; COMPND 5 EC: 4.1.1.49; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: PCKA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K12; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PHOSPHOENOLPYRUVATE CARBOXYKINASE, ACTIVE SITE LYSINE, TETRAHEDRAL KEYWDS 2 MANGANESE COORDINATION, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR L.T.J.DELBAERE,J.J.H.COTELESAGE,H.GOLDIE REVDAT 5 30-AUG-23 2PY7 1 REMARK REVDAT 4 20-OCT-21 2PY7 1 REMARK SEQADV REVDAT 3 13-JUL-11 2PY7 1 VERSN REVDAT 2 24-FEB-09 2PY7 1 VERSN REVDAT 1 22-APR-08 2PY7 0 JRNL AUTH L.T.J.DELBAERE,J.J.H.COTELESAGE,H.GOLDIE JRNL TITL CRYSTAL STRUCTURE OF E. COLI PHOSPHOENOLPYRUVATE JRNL TITL 2 CARBOXYKINASE MUTANT LYS213SER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 24587 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1282 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1481 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.1720 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4133 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.324 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.218 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.132 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.075 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4264 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5802 ; 1.234 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 534 ; 5.684 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 188 ;33.833 ;24.309 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 680 ;13.948 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;16.456 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 641 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3253 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2259 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2935 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 485 ; 0.164 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.107 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 50 ; 0.168 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 44 ; 0.300 ; 0.200 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): 2728 ; 0.523 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4268 ; 0.869 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1766 ; 1.372 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1534 ; 2.205 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2PY7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000042914. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.919 REMARK 200 MONOCHROMATOR : DIAMOND (111) DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR BENT CYLINDRICAL REMARK 200 SI-MIRROR (RH COATING) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36560 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 13.960 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 200 DATA REDUNDANCY : 2.950 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10000 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.17 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.14000 REMARK 200 FOR SHELL : 4.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1AYL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A 2UL DROP WITH 4 MG/ML PROTEIN, 20 MM REMARK 280 TRIS-HCL (PH 7.6), 0.5 MM EDTA, 5 MM ADP, 2.5 MM REMARK 280 PHOSPHOENOLPYRUVATE, 2.5 MM MGCL2, 2.5 MM MNCL2, 0.1 M SODIUM REMARK 280 ACETATE, 0.05 M SODIUM CACODYLATE (PH 6.5), 15% PEG 8000 WAS REMARK 280 ALLOWED TO EQUILIBRATE WITH A 1 ML WELL OF 0.2 M SODIUM ACEATE, REMARK 280 0.1 M SODIUM CACODYLATE 30% PEG 8000. AFTER A WEEK A 0.1 X 0.1 X REMARK 280 0.4 MM CRYSTAL WAS REMOVED AND PUT IN A SMALL VOLUME OF WELL REMARK 280 SOLUTION WITH 30% GLYCEROL ADDED. THE CRYSTAL WAS PUT INTO A REMARK 280 LOOP AND FLASH COOLED IN LIQUID NOTROGEN, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 62.49950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.83150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 62.49950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 47.83150 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 APPLY THE FOLLOWING TO CHAINS: X 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH X1114 LIES ON A SPECIAL POSITION. REMARK 375 HOH X1183 LIES ON A SPECIAL POSITION. REMARK 375 HOH X1211 LIES ON A SPECIAL POSITION. REMARK 375 HOH X1329 LIES ON A SPECIAL POSITION. REMARK 375 HOH X1448 LIES ON A SPECIAL POSITION. REMARK 375 HOH X1509 LIES ON A SPECIAL POSITION. REMARK 375 HOH X1517 LIES ON A SPECIAL POSITION. 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 X 1 REMARK 465 ARG X 2 REMARK 465 VAL X 3 REMARK 465 ASN X 4 REMARK 465 ASN X 5 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN X 10 CG CD OE1 NE2 REMARK 470 GLU X 11 CG CD OE1 OE2 REMARK 470 ASP X 22 CG OD1 OD2 REMARK 470 GLU X 239 CG CD OE1 OE2 REMARK 470 LYS X 240 CG CD CE NZ REMARK 470 GLU X 317 CG CD OE1 OE2 REMARK 470 LYS X 453 CG CD CE NZ 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 X 1468 O HOH X 1482 1.80 REMARK 500 O HOH X 1129 O HOH X 1535 1.93 REMARK 500 O HOH X 1215 O HOH X 1482 1.97 REMARK 500 CB THR X 499 O HOH X 1456 2.07 REMARK 500 O HOH X 1195 O HOH X 1548 2.10 REMARK 500 ND2 ASN X 444 O HOH X 1050 2.13 REMARK 500 O HOH X 1309 O HOH X 1425 2.14 REMARK 500 N THR X 446 O HOH X 1456 2.14 REMARK 500 CG ASN X 444 O HOH X 1050 2.17 REMARK 500 CE1 HIS X 382 O HOH X 1558 2.19 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 O HOH X 1381 O HOH X 1483 1554 1.68 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 ASP X 269 -28.87 -155.64 REMARK 500 ASP X 274 -165.13 -109.26 REMARK 500 ASP X 307 -14.32 94.55 REMARK 500 ASN X 331 38.18 -88.50 REMARK 500 MET X 477 -56.11 73.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 998 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN X 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN X 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP X 541 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AYL RELATED DB: PDB REMARK 900 RELATED ID: 2PXZ RELATED DB: PDB DBREF 2PY7 X 1 540 UNP P22259 PPCK_ECOLI 1 540 SEQADV 2PY7 SER X 213 UNP P22259 LYS 213 ENGINEERED MUTATION SEQRES 1 X 540 MET ARG VAL ASN ASN GLY LEU THR PRO GLN GLU LEU GLU SEQRES 2 X 540 ALA TYR GLY ILE SER ASP VAL HIS ASP ILE VAL TYR ASN SEQRES 3 X 540 PRO SER TYR ASP LEU LEU TYR GLN GLU GLU LEU ASP PRO SEQRES 4 X 540 SER LEU THR GLY TYR GLU ARG GLY VAL LEU THR ASN LEU SEQRES 5 X 540 GLY ALA VAL ALA VAL ASP THR GLY ILE PHE THR GLY ARG SEQRES 6 X 540 SER PRO LYS ASP LYS TYR ILE VAL ARG ASP ASP THR THR SEQRES 7 X 540 ARG ASP THR PHE TRP TRP ALA ASP LYS GLY LYS GLY LYS SEQRES 8 X 540 ASN ASP ASN LYS PRO LEU SER PRO GLU THR TRP GLN HIS SEQRES 9 X 540 LEU LYS GLY LEU VAL THR ARG GLN LEU SER GLY LYS ARG SEQRES 10 X 540 LEU PHE VAL VAL ASP ALA PHE CYS GLY ALA ASN PRO ASP SEQRES 11 X 540 THR ARG LEU SER VAL ARG PHE ILE THR GLU VAL ALA TRP SEQRES 12 X 540 GLN ALA HIS PHE VAL LYS ASN MET PHE ILE ARG PRO SER SEQRES 13 X 540 ASP GLU GLU LEU ALA GLY PHE LYS PRO ASP PHE ILE VAL SEQRES 14 X 540 MET ASN GLY ALA LYS CYS THR ASN PRO GLN TRP LYS GLU SEQRES 15 X 540 GLN GLY LEU ASN SER GLU ASN PHE VAL ALA PHE ASN LEU SEQRES 16 X 540 THR GLU ARG MET GLN LEU ILE GLY GLY THR TRP TYR GLY SEQRES 17 X 540 GLY GLU MET LYS SER GLY MET PHE SER MET MET ASN TYR SEQRES 18 X 540 LEU LEU PRO LEU LYS GLY ILE ALA SER MET HIS CYS SER SEQRES 19 X 540 ALA ASN VAL GLY GLU LYS GLY ASP VAL ALA VAL PHE PHE SEQRES 20 X 540 GLY LEU SER GLY THR GLY LYS THR THR LEU SER THR ASP SEQRES 21 X 540 PRO LYS ARG ARG LEU ILE GLY ASP ASP GLU HIS GLY TRP SEQRES 22 X 540 ASP ASP ASP GLY VAL PHE ASN PHE GLU GLY GLY CYS TYR SEQRES 23 X 540 ALA LYS THR ILE LYS LEU SER LYS GLU ALA GLU PRO GLU SEQRES 24 X 540 ILE TYR ASN ALA ILE ARG ARG ASP ALA LEU LEU GLU ASN SEQRES 25 X 540 VAL THR VAL ARG GLU ASP GLY THR ILE ASP PHE ASP ASP SEQRES 26 X 540 GLY SER LYS THR GLU ASN THR ARG VAL SER TYR PRO ILE SEQRES 27 X 540 TYR HIS ILE ASP ASN ILE VAL LYS PRO VAL SER LYS ALA SEQRES 28 X 540 GLY HIS ALA THR LYS VAL ILE PHE LEU THR ALA ASP ALA SEQRES 29 X 540 PHE GLY VAL LEU PRO PRO VAL SER ARG LEU THR ALA ASP SEQRES 30 X 540 GLN THR GLN TYR HIS PHE LEU SER GLY PHE THR ALA LYS SEQRES 31 X 540 LEU ALA GLY THR GLU ARG GLY ILE THR GLU PRO THR PRO SEQRES 32 X 540 THR PHE SER ALA CYS PHE GLY ALA ALA PHE LEU SER LEU SEQRES 33 X 540 HIS PRO THR GLN TYR ALA GLU VAL LEU VAL LYS ARG MET SEQRES 34 X 540 GLN ALA ALA GLY ALA GLN ALA TYR LEU VAL ASN THR GLY SEQRES 35 X 540 TRP ASN GLY THR GLY LYS ARG ILE SER ILE LYS ASP THR SEQRES 36 X 540 ARG ALA ILE ILE ASP ALA ILE LEU ASN GLY SER LEU ASP SEQRES 37 X 540 ASN ALA GLU THR PHE THR LEU PRO MET PHE ASN LEU ALA SEQRES 38 X 540 ILE PRO THR GLU LEU PRO GLY VAL ASP THR LYS ILE LEU SEQRES 39 X 540 ASP PRO ARG ASN THR TYR ALA SER PRO GLU GLN TRP GLN SEQRES 40 X 540 GLU LYS ALA GLU THR LEU ALA LYS LEU PHE ILE ASP ASN SEQRES 41 X 540 PHE ASP LYS TYR THR ASP THR PRO ALA GLY ALA ALA LEU SEQRES 42 X 540 VAL ALA ALA GLY PRO LYS LEU HET MG X 998 1 HET MN X 999 1 HET MN X1001 1 HET ATP X 541 31 HETNAM MG MAGNESIUM ION HETNAM MN MANGANESE (II) ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 MN 2(MN 2+) FORMUL 5 ATP C10 H16 N5 O13 P3 FORMUL 6 HOH *570(H2 O) HELIX 1 1 THR X 8 ALA X 14 1 7 HELIX 2 2 SER X 28 ASP X 38 1 11 HELIX 3 3 THR X 42 GLU X 45 5 4 HELIX 4 4 SER X 66 LYS X 68 5 3 HELIX 5 5 SER X 98 SER X 114 1 17 HELIX 6 6 VAL X 141 PHE X 152 1 12 HELIX 7 7 SER X 156 GLY X 162 1 7 HELIX 8 8 GLY X 208 LEU X 223 1 16 HELIX 9 9 PRO X 224 GLY X 227 5 4 HELIX 10 10 GLY X 253 THR X 259 1 7 HELIX 11 11 GLU X 297 ILE X 304 1 8 HELIX 12 12 TYR X 339 ILE X 341 5 3 HELIX 13 13 THR X 375 GLY X 386 1 12 HELIX 14 14 GLY X 393 GLY X 397 5 5 HELIX 15 15 ALA X 407 LEU X 414 5 8 HELIX 16 16 HIS X 417 GLY X 433 1 17 HELIX 17 17 SER X 451 GLY X 465 1 15 HELIX 18 18 GLY X 465 ALA X 470 1 6 HELIX 19 19 THR X 491 TYR X 500 5 10 HELIX 20 20 SER X 502 ASP X 522 1 21 HELIX 21 21 LYS X 523 THR X 525 5 3 HELIX 22 22 THR X 527 VAL X 534 1 8 HELIX 23 23 ALA X 535 GLY X 537 5 3 SHEET 1 A 8 ILE X 23 TYR X 25 0 SHEET 2 A 8 LEU X 118 CYS X 125 1 O LEU X 118 N VAL X 24 SHEET 3 A 8 LEU X 133 THR X 139 -1 O THR X 139 N PHE X 119 SHEET 4 A 8 PHE X 167 GLY X 172 1 O ASN X 171 N ILE X 138 SHEET 5 A 8 MET X 199 GLY X 203 1 O GLN X 200 N MET X 170 SHEET 6 A 8 PHE X 190 ASN X 194 -1 N ALA X 192 O LEU X 201 SHEET 7 A 8 LYS X 70 VAL X 73 1 N VAL X 73 O PHE X 193 SHEET 8 A 8 LYS X 95 LEU X 97 1 O LYS X 95 N ILE X 72 SHEET 1 B 5 GLY X 47 LEU X 49 0 SHEET 2 B 5 VAL X 55 VAL X 57 -1 O ALA X 56 N VAL X 48 SHEET 3 B 5 LEU X 309 GLU X 311 1 O LEU X 310 N VAL X 55 SHEET 4 B 5 ARG X 333 PRO X 337 -1 O SER X 335 N LEU X 309 SHEET 5 B 5 GLY X 284 LYS X 288 -1 N CYS X 285 O TYR X 336 SHEET 1 C 4 ARG X 264 GLY X 267 0 SHEET 2 C 4 ALA X 229 VAL X 237 -1 N VAL X 237 O ARG X 264 SHEET 3 C 4 GLU X 270 ASP X 274 -1 O HIS X 271 N MET X 231 SHEET 4 C 4 GLY X 277 ASN X 280 -1 O PHE X 279 N GLY X 272 SHEET 1 D 6 ARG X 264 GLY X 267 0 SHEET 2 D 6 ALA X 229 VAL X 237 -1 N VAL X 237 O ARG X 264 SHEET 3 D 6 VAL X 243 GLY X 248 -1 O ALA X 244 N ASN X 236 SHEET 4 D 6 ALA X 354 THR X 361 1 O ILE X 358 N VAL X 245 SHEET 5 D 6 GLN X 435 ASN X 440 1 O TYR X 437 N PHE X 359 SHEET 6 D 6 VAL X 371 ARG X 373 -1 N SER X 372 O LEU X 438 SHEET 1 E 2 THR X 314 VAL X 315 0 SHEET 2 E 2 ILE X 321 ASP X 322 -1 O ASP X 322 N THR X 314 SHEET 1 F 2 PHE X 387 LEU X 391 0 SHEET 2 F 2 PRO X 401 PHE X 405 -1 O THR X 404 N THR X 388 SHEET 1 G 2 THR X 472 LEU X 475 0 SHEET 2 G 2 LEU X 480 PRO X 483 -1 O LEU X 480 N LEU X 475 CISPEP 1 LYS X 346 PRO X 347 0 3.96 SITE 1 AC1 4 THR X 255 HOH X1012 HOH X1022 HOH X1040 SITE 1 AC2 3 HIS X 232 ASP X 269 HOH X1373 SITE 1 AC3 4 ASP X 19 HIS X 21 HIS X 104 HOH X1488 SITE 1 AC4 28 HIS X 232 LEU X 249 SER X 250 GLY X 251 SITE 2 AC4 28 THR X 252 GLY X 253 LYS X 254 THR X 255 SITE 3 AC4 28 THR X 256 ASP X 269 LYS X 288 GLU X 297 SITE 4 AC4 28 ARG X 333 THR X 441 ARG X 449 ILE X 450 SITE 5 AC4 28 SER X 451 ILE X 452 THR X 455 HOH X1012 SITE 6 AC4 28 HOH X1022 HOH X1040 HOH X1100 HOH X1130 SITE 7 AC4 28 HOH X1230 HOH X1327 HOH X1375 HOH X1384 CRYST1 124.999 95.663 46.319 90.00 96.12 90.00 C 1 2 1 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 0.008000 0.000000 0.000857 0.00000 SCALE2 0.000000 0.010453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021713 0.00000