HEADER LYASE 14-MAY-07 2PXZ TITLE E. COLI PHOSPHOENOLPYRUVATE CARBOXYKINASE (PEPCK) COMPLEXED WITH ATP, TITLE 2 MG2+, MN2+, CARBON DIOXIDE AND OXALOACETATE 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 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 P-LOOP, OXALOACETATE, CARBON DIOXIDE, CO2, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR L.T.J.DELBAERE,J.J.H.COTELESAGE,H.GOLDIE REVDAT 4 21-FEB-24 2PXZ 1 REMARK REVDAT 3 13-JUL-11 2PXZ 1 VERSN REVDAT 2 24-FEB-09 2PXZ 1 VERSN REVDAT 1 22-APR-08 2PXZ 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 (PEPCK) COMPLEXED WITH ATP, MG2+, MN2+, CARBON JRNL TITL 3 DIOXIDE AND OXALOACETATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.23 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) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24889 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1322 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) : 2.23 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1834 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1790 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4007 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 283 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.32 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) : 0.02000 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): 0.297 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.221 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.147 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.689 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4144 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5646 ; 1.932 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 524 ; 7.025 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;35.049 ;24.190 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 625 ;15.914 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;16.591 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 631 ; 0.143 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3176 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1908 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2817 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 293 ; 0.174 ; 0.200 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): 33 ; 0.240 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.374 ; 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): 2689 ; 1.047 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4172 ; 1.653 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1694 ; 2.767 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1474 ; 4.049 ; 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 2PXZ 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_1000042906. 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 : 4.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3317 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 : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 171743 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 47.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 13.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8UL DROP WITH 8UG/ML PROTEIN, 2MM ADP, REMARK 280 5MM MGCL2, 10 UM MNCL2, 1 MM EDTA, 100 MM SODIUM ACETATE (PH 4.4) REMARK 280 , 200 MM AMMONIUM ACETATE AND 12% W/V PEG 4000 WAS ALLOWED TO REMARK 280 EQUILIBRATE WITH A 1 ML RESERVOIR OF 100 MM SODIUM ACEATE, 200 REMARK 280 MM AMMONIUM ACETATE AND 27% PEG 4000. AFTER CRYSTALS GREW FOR REMARK 280 ONE WEEK 2UL OF A 1 MM EDTA AND SATURATED SODIUM OXALOACETATE REMARK 280 SOLUTION WAS ADDED TO THE DROP. 5 UL OF GLYCEROL WAS ADDED TO REMARK 280 THE DROP. A 0.1 X 0.1 X 0.3 MM CRYSTAL WAS REMOVED WITH A LOOP REMARK 280 AND FLASH COOLED IN LIQUID NITROGEN, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 294K 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 62.27800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.15100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 62.27800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 47.15100 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 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 465 GLY X 6 REMARK 465 LEU X 7 REMARK 465 THR X 8 REMARK 465 THR X 394 REMARK 465 GLU X 395 REMARK 465 ARG X 396 REMARK 465 GLY X 397 REMARK 465 ILE X 398 REMARK 465 THR X 399 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 PRO X 9 CG CD REMARK 470 GLU X 11 CG CD OE1 OE2 REMARK 470 GLU X 13 CG CD OE1 OE2 REMARK 470 LYS X 89 CG CD CE NZ REMARK 470 LYS X 91 CG CD CE NZ REMARK 470 SER X 156 OG REMARK 470 GLU X 158 CG CD OE1 OE2 REMARK 470 LYS X 164 CG CD CE NZ REMARK 470 GLU X 182 CG CD OE1 OE2 REMARK 470 GLU X 239 CG CD OE1 OE2 REMARK 470 LYS X 240 CG CD CE NZ REMARK 470 LYS X 262 CG CD CE NZ REMARK 470 LYS X 294 CG CD CE NZ REMARK 470 GLU X 295 CG CD OE1 OE2 REMARK 470 GLU X 317 CG CD OE1 OE2 REMARK 470 ARG X 373 CG CD NE CZ NH1 NH2 REMARK 470 LYS X 390 CG CD CE NZ REMARK 470 GLU X 400 CG CD OE1 OE2 REMARK 470 LYS X 453 CG CD CE NZ REMARK 470 ASN X 469 CG OD1 ND2 REMARK 470 GLU X 471 CG CD OE1 OE2 REMARK 470 LYS X 509 CG CD CE NZ REMARK 470 LYS X 515 CG CD CE NZ REMARK 470 ASP X 526 CG OD1 OD2 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 O5 OAA X 701 O HOH X 801 1.95 REMARK 500 OG1 THR X 474 O HOH X 857 2.15 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 712 O HOH X 712 2656 1.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR X 71 C ILE X 72 N -0.148 REMARK 500 ASN X 302 CB ASN X 302 CG 0.140 REMARK 500 VAL X 426 C LYS X 427 N -0.209 REMARK 500 LYS X 427 C ARG X 428 N -0.149 REMARK 500 TYR X 437 C LEU X 438 N -0.180 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 PRO X 9 N - CA - CB ANGL. DEV. = 8.5 DEGREES REMARK 500 ILE X 72 CA - C - N ANGL. DEV. = 20.2 DEGREES REMARK 500 ILE X 72 O - C - N ANGL. DEV. = -18.8 DEGREES REMARK 500 ARG X 111 CG - CD - NE ANGL. DEV. = -13.1 DEGREES REMARK 500 ARG X 111 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG X 111 NE - CZ - NH2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG X 117 NE - CZ - NH1 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG X 198 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 TYR X 437 CA - C - N ANGL. DEV. = 25.6 DEGREES REMARK 500 TYR X 437 O - C - N ANGL. DEV. = -23.7 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 LYS X 91 108.76 61.97 REMARK 500 SER X 156 159.99 -48.99 REMARK 500 ASP X 269 -40.63 -151.11 REMARK 500 ASP X 274 -163.60 -115.72 REMARK 500 ASP X 307 -15.75 93.44 REMARK 500 ASN X 331 41.10 -88.79 REMARK 500 MET X 477 -63.67 75.30 REMARK 500 ALA X 529 -67.57 81.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ILE X 72 11.77 REMARK 500 LYS X 427 10.30 REMARK 500 TYR X 437 16.35 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 543 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN X 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OAA X 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP X 541 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO2 X 656 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AYL RELATED DB: PDB REMARK 900 RELATED ID: 2PY7 RELATED DB: PDB DBREF 2PXZ X 1 540 UNP P22259 PPCK_ECOLI 1 540 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 LYS 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 543 1 HET MN X 700 1 HET OAA X 701 9 HET ATP X 541 31 HET CO2 X 656 6 HETNAM MG MAGNESIUM ION HETNAM MN MANGANESE (II) ION HETNAM OAA OXALOACETATE ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM CO2 CARBON DIOXIDE FORMUL 2 MG MG 2+ FORMUL 3 MN MN 2+ FORMUL 4 OAA C4 H3 O5 1- FORMUL 5 ATP C10 H16 N5 O13 P3 FORMUL 6 CO2 C O2 FORMUL 7 HOH *283(H2 O) HELIX 1 1 PRO X 9 TYR X 15 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 LYS X 226 1 19 HELIX 9 9 GLY X 253 THR X 259 1 7 HELIX 10 10 GLU X 297 ILE X 304 1 8 HELIX 11 11 TYR X 339 ILE X 341 5 3 HELIX 12 12 THR X 375 GLY X 386 1 12 HELIX 13 13 ALA X 407 LEU X 414 5 8 HELIX 14 14 HIS X 417 VAL X 426 1 10 HELIX 15 15 LYS X 427 LYS X 427 1 1 HELIX 16 16 ARG X 428 GLY X 433 1 6 HELIX 17 17 SER X 451 ASN X 464 1 14 HELIX 18 18 ASP X 490 LEU X 494 5 5 HELIX 19 19 ASP X 495 TYR X 500 5 6 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 ALA X 529 VAL X 534 1 6 HELIX 23 23 ALA X 535 GLY X 537 5 3 SHEET 1 A 7 ILE X 23 TYR X 25 0 SHEET 2 A 7 LEU X 118 CYS X 125 1 O LEU X 118 N VAL X 24 SHEET 3 A 7 LEU X 133 THR X 139 -1 O THR X 139 N PHE X 119 SHEET 4 A 7 PHE X 167 GLY X 172 1 O ASN X 171 N ILE X 138 SHEET 5 A 7 MET X 199 GLY X 203 1 O GLN X 200 N MET X 170 SHEET 6 A 7 PHE X 190 ASN X 194 -1 N ASN X 194 O MET X 199 SHEET 7 A 7 LYS X 70 ILE X 72 1 N TYR X 71 O VAL X 191 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 57 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 TRP X 273 -1 O HIS X 271 N MET X 231 SHEET 4 C 4 VAL X 278 ASN X 280 -1 O PHE X 279 N GLY X 272 SHEET 1 D 5 ARG X 264 GLY X 267 0 SHEET 2 D 5 ALA X 229 VAL X 237 -1 N VAL X 237 O ARG X 264 SHEET 3 D 5 VAL X 243 PHE X 247 -1 O ALA X 244 N ASN X 236 SHEET 4 D 5 ALA X 354 THR X 361 1 O ILE X 358 N PHE X 247 SHEET 5 D 5 GLN X 435 ASN X 440 1 O VAL X 439 N PHE X 359 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 402 N LYS X 390 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 -0.57 SITE 1 AC1 4 THR X 255 HOH X 831 HOH X 832 HOH X 833 SITE 1 AC2 5 LYS X 213 HIS X 232 ASP X 269 HOH X 928 SITE 2 AC2 5 HOH X 966 SITE 1 AC3 9 HIS X 232 LEU X 249 SER X 250 THR X 388 SITE 2 AC3 9 PHE X 413 HOH X 801 HOH X 929 HOH X 966 SITE 3 AC3 9 HOH X 983 SITE 1 AC4 27 HIS X 232 LEU X 249 SER X 250 GLY X 251 SITE 2 AC4 27 THR X 252 GLY X 253 LYS X 254 THR X 255 SITE 3 AC4 27 THR X 256 ASP X 269 LYS X 288 GLU X 297 SITE 4 AC4 27 ARG X 333 THR X 441 ARG X 449 ILE X 450 SITE 5 AC4 27 SER X 451 ILE X 452 THR X 455 HOH X 750 SITE 6 AC4 27 HOH X 770 HOH X 831 HOH X 832 HOH X 833 SITE 7 AC4 27 HOH X 928 HOH X 937 HOH X 966 SITE 1 AC5 6 ARG X 65 TYR X 207 GLY X 209 LYS X 213 SITE 2 AC5 6 HOH X 795 HOH X 928 CRYST1 124.556 94.302 46.354 90.00 95.54 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 0.008029 0.000000 0.000779 0.00000 SCALE2 0.000000 0.010604 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021674 0.00000