HEADER ISOMERASE 06-MAY-14 4QAX TITLE CRYSTAL STRUCTURE OF POST-CATALYTIC BINARY COMPLEX OF PHOSPHOGLYCERATE TITLE 2 MUTASE FROM STAPHYLOCOCCUS AUREUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2,3-BISPHOSPHOGLYCERATE-INDEPENDENT PHOSPHOGLYCERATE COMPND 3 MUTASE; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 3-505; COMPND 6 SYNONYM: BPG-INDEPENDENT PGAM, PHOSPHOGLYCEROMUTASE, IPGM; COMPND 7 EC: 5.4.2.12; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS; SOURCE 3 ORGANISM_TAXID: 93061; SOURCE 4 STRAIN: NCTC 8325; SOURCE 5 GENE: GPMI, SAOUHSC_00798; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS 2, 3-BISPHOSPHOGLYCERATE INDEPENDENT PHOSPHOGLYCERATE MUTASE., KEYWDS 2 GLYCOLYSIS AND GLUCONEOGENESIS, CYTOSOL, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.ROYCHOWDHURY,A.KUNDU,M.BOSE,A.GUJAR,A.K.DAS REVDAT 2 08-NOV-23 4QAX 1 REMARK SEQADV LINK REVDAT 1 06-MAY-15 4QAX 0 JRNL AUTH A.ROYCHOWDHURY,A.KUNDU,M.BOSE,A.GUJAR,S.MUKHERJEE,A.K.DAS JRNL TITL STRUCTURAL AND FUNCCTIONAL ANALYSIS OF PHOSPHOGLYCERATE JRNL TITL 2 MUTASE FROM STAPHYLOCOCCUS AUREUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 35796 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1787 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2323 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE SET COUNT : 129 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3934 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 288 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.64000 REMARK 3 B22 (A**2) : 0.42000 REMARK 3 B33 (A**2) : -1.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.169 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.805 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4019 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3746 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5446 ; 1.980 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8617 ; 1.014 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 502 ; 6.966 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 206 ;39.166 ;25.340 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 673 ;16.737 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;21.251 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 602 ; 0.170 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4657 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 914 ; 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 : 1 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 3 A 505 REMARK 3 ORIGIN FOR THE GROUP (A): 20.1824 -10.9296 6.2558 REMARK 3 T TENSOR REMARK 3 T11: 0.0074 T22: 0.0459 REMARK 3 T33: 0.0085 T12: -0.0015 REMARK 3 T13: -0.0048 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.0370 L22: 0.3809 REMARK 3 L33: 0.1892 L12: 0.0661 REMARK 3 L13: -0.0809 L23: -0.1166 REMARK 3 S TENSOR REMARK 3 S11: 0.0055 S12: 0.0028 S13: -0.0035 REMARK 3 S21: 0.0268 S22: -0.0150 S23: 0.0119 REMARK 3 S31: -0.0162 S32: 0.0104 S33: 0.0095 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: NULL REMARK 4 REMARK 4 4QAX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085824. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : VARIMAX, OSMIC MIRROR REMARK 200 OPTICS : VARIMAX, OSMIC MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35850 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 59.855 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 22.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.35600 REMARK 200 R SYM FOR SHELL (I) : 0.35600 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.0.05 REMARK 200 STARTING MODEL: 4MY4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM CHLORIDE, 0.1M BIS TRIS PH REMARK 280 6.5, 25%(W/V)POLYETHYLENEGLYCOL 3350. , VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 36.40100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.62700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.34450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.62700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.40100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.34450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 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 GLU A 87 CG CD OE1 OE2 REMARK 470 GLU A 142 CG CD OE1 OE2 REMARK 470 LYS A 143 CE NZ REMARK 470 ARG A 271 CD NE CZ NH1 NH2 REMARK 470 GLU A 279 CG CD OE1 OE2 REMARK 470 LYS A 347 CD CE NZ REMARK 470 GLN A 451 CG CD OE1 NE2 REMARK 470 GLU A 495 CD OE1 OE2 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 NH2 ARG A 257 O2 2PG A 603 1.91 REMARK 500 CD ARG A 260 O1 2PG A 603 2.10 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 A 821 O HOH A 930 4445 1.39 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 ARG A 17 CD - NE - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 17 NE - CZ - NH2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ARG A 35 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 35 NE - CZ - NH2 ANGL. DEV. = 4.9 DEGREES REMARK 500 THR A 42 N - CA - CB ANGL. DEV. = -11.8 DEGREES REMARK 500 ARG A 153 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 185 NE - CZ - NH1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 185 NE - CZ - NH2 ANGL. DEV. = -8.3 DEGREES REMARK 500 ARG A 206 NE - CZ - NH1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 206 NE - CZ - NH2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ASP A 243 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 259 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 260 CD - NE - CZ ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG A 260 NE - CZ - NH1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 260 NE - CZ - NH2 ANGL. DEV. = -8.4 DEGREES REMARK 500 VAL A 334 CG1 - CB - CG2 ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG A 350 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 350 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 LEU A 391 CB - CG - CD2 ANGL. DEV. = 12.0 DEGREES REMARK 500 LEU A 481 CB - CG - CD1 ANGL. DEV. = 12.3 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 SER A 109 -157.81 -116.33 REMARK 500 GLU A 142 -73.81 93.12 REMARK 500 ASP A 151 -90.86 -96.07 REMARK 500 PHE A 208 -126.93 -83.91 REMARK 500 THR A 335 -97.34 -103.27 REMARK 500 MET A 368 -130.25 39.83 REMARK 500 THR A 436 -159.72 -159.86 REMARK 500 HIS A 439 171.14 159.81 REMARK 500 ASN A 441 -64.83 -169.95 REMARK 500 THR A 466 55.08 -91.21 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 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 12 OD1 REMARK 620 2 SER A 62 OG 114.1 REMARK 620 3 ASP A 438 OD1 112.6 110.1 REMARK 620 4 HIS A 439 NE2 106.1 111.7 101.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 397 OD1 REMARK 620 2 HIS A 401 NE2 101.6 REMARK 620 3 HIS A 456 NE2 106.4 92.2 REMARK 620 4 HOH A 701 O 89.7 88.1 163.5 REMARK 620 5 HOH A 702 O 89.9 165.8 92.6 83.6 REMARK 620 6 HOH A 703 O 163.0 90.7 84.4 79.0 76.4 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2PG A 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MY4 RELATED DB: PDB REMARK 900 RELATED ID: 4NWJ RELATED DB: PDB REMARK 900 RELATED ID: 4NWX RELATED DB: PDB DBREF 4QAX A 1 505 UNP Q2G029 Q2G029_STAA8 1 505 SEQADV 4QAX HIS A -7 UNP Q2G029 EXPRESSION TAG SEQADV 4QAX HIS A -6 UNP Q2G029 EXPRESSION TAG SEQADV 4QAX HIS A -5 UNP Q2G029 EXPRESSION TAG SEQADV 4QAX HIS A -4 UNP Q2G029 EXPRESSION TAG SEQADV 4QAX HIS A -3 UNP Q2G029 EXPRESSION TAG SEQADV 4QAX HIS A -2 UNP Q2G029 EXPRESSION TAG SEQADV 4QAX GLY A -1 UNP Q2G029 EXPRESSION TAG SEQADV 4QAX SER A 0 UNP Q2G029 EXPRESSION TAG SEQRES 1 A 513 HIS HIS HIS HIS HIS HIS GLY SER MET ALA LYS LYS PRO SEQRES 2 A 513 THR ALA LEU ILE ILE LEU ASP GLY PHE ALA ASN ARG GLU SEQRES 3 A 513 SER GLU HIS GLY ASN ALA VAL LYS LEU ALA ASN LYS PRO SEQRES 4 A 513 ASN PHE ASP ARG TYR TYR ASN LYS TYR PRO THR THR GLN SEQRES 5 A 513 ILE GLU ALA SER GLY LEU ASP VAL GLY LEU PRO GLU GLY SEQRES 6 A 513 GLN MET GLY ASN SER GLU VAL GLY HIS MET ASN ILE GLY SEQRES 7 A 513 ALA GLY ARG ILE VAL TYR GLN SER LEU THR ARG ILE ASN SEQRES 8 A 513 LYS SER ILE GLU ASP GLY ASP PHE PHE GLU ASN ASP VAL SEQRES 9 A 513 LEU ASN ASN ALA ILE ALA HIS VAL ASN SER HIS ASP SER SEQRES 10 A 513 ALA LEU HIS ILE PHE GLY LEU LEU SER ASP GLY GLY VAL SEQRES 11 A 513 HIS SER HIS TYR LYS HIS LEU PHE ALA LEU LEU GLU LEU SEQRES 12 A 513 ALA LYS LYS GLN GLY VAL GLU LYS VAL TYR VAL HIS ALA SEQRES 13 A 513 PHE LEU ASP GLY ARG ASP VAL ASP GLN LYS SER ALA LEU SEQRES 14 A 513 LYS TYR ILE GLU GLU THR GLU ALA LYS PHE ASN GLU LEU SEQRES 15 A 513 GLY ILE GLY GLN PHE ALA SER VAL SER GLY ARG TYR TYR SEQRES 16 A 513 ALA MET ASP ARG ASP LYS ARG TRP GLU ARG GLU GLU LYS SEQRES 17 A 513 ALA TYR ASN ALA ILE ARG ASN PHE ASP ALA PRO THR TYR SEQRES 18 A 513 ALA THR ALA LYS GLU GLY VAL GLU ALA SER TYR ASN GLU SEQRES 19 A 513 GLY LEU THR ASP GLU PHE VAL VAL PRO PHE ILE VAL GLU SEQRES 20 A 513 ASN GLN ASN ASP GLY VAL ASN ASP GLY ASP ALA VAL ILE SEQRES 21 A 513 PHE TYR ASN PHE ARG PRO ASP ARG ALA ALA GLN LEU SER SEQRES 22 A 513 GLU ILE PHE ALA ASN ARG ALA PHE GLU GLY PHE LYS VAL SEQRES 23 A 513 GLU GLN VAL LYS ASP LEU PHE TYR ALA THR PHE THR LYS SEQRES 24 A 513 TYR ASN ASP ASN ILE ASP ALA ALA ILE VAL PHE GLU LYS SEQRES 25 A 513 VAL ASP LEU ASN ASN THR ILE GLY GLU ILE ALA GLN ASN SEQRES 26 A 513 ASN ASN LEU THR GLN LEU ARG ILE ALA GLU THR GLU LYS SEQRES 27 A 513 TYR PRO HIS VAL THR TYR PHE MET SER GLY GLY ARG ASN SEQRES 28 A 513 GLU GLU PHE LYS GLY GLU ARG ARG ARG LEU ILE ASP SER SEQRES 29 A 513 PRO LYS VAL ALA THR TYR ASP LEU LYS PRO GLU MET SER SEQRES 30 A 513 ALA TYR GLU VAL LYS ASP ALA LEU LEU GLU GLU LEU ASN SEQRES 31 A 513 LYS GLY ASP LEU ASP LEU ILE ILE LEU ASN PHE ALA ASN SEQRES 32 A 513 PRO ASP MET VAL GLY HIS SER GLY MET LEU GLU PRO THR SEQRES 33 A 513 ILE LYS ALA ILE GLU ALA VAL ASP GLU CYS LEU GLY GLU SEQRES 34 A 513 VAL VAL ASP LYS ILE LEU ASP MET ASP GLY TYR ALA ILE SEQRES 35 A 513 ILE THR ALA ASP HIS GLY ASN SER ASP GLN VAL LEU THR SEQRES 36 A 513 ASP ASP ASP GLN PRO MET THR THR HIS THR THR ASN PRO SEQRES 37 A 513 VAL PRO VAL ILE VAL THR LYS GLU GLY VAL THR LEU ARG SEQRES 38 A 513 GLU THR GLY ARG LEU GLY ASP LEU ALA PRO THR LEU LEU SEQRES 39 A 513 ASP LEU LEU ASN VAL GLU GLN PRO GLU ASP MET THR GLY SEQRES 40 A 513 GLU SER LEU ILE LYS HIS HET MN A 601 1 HET MN A 602 1 HET 2PG A 603 11 HETNAM MN MANGANESE (II) ION HETNAM 2PG 2-PHOSPHOGLYCERIC ACID FORMUL 2 MN 2(MN 2+) FORMUL 4 2PG C3 H7 O7 P FORMUL 5 HOH *288(H2 O) HELIX 1 1 ASN A 23 ALA A 28 1 6 HELIX 2 2 LYS A 30 TYR A 40 1 11 HELIX 3 3 SER A 48 GLY A 53 5 6 HELIX 4 4 ASN A 61 GLY A 72 1 12 HELIX 5 5 GLN A 77 GLY A 89 1 13 HELIX 6 6 ASP A 90 GLU A 93 5 4 HELIX 7 7 ASN A 94 ASP A 108 1 15 HELIX 8 8 HIS A 125 GLN A 139 1 15 HELIX 9 9 SER A 159 GLY A 175 1 17 HELIX 10 10 ARG A 185 MET A 189 1 5 HELIX 11 11 ARG A 194 ARG A 206 1 13 HELIX 12 12 THR A 215 GLU A 226 1 12 HELIX 13 13 THR A 229 VAL A 233 5 5 HELIX 14 14 ARG A 257 ASN A 270 1 14 HELIX 15 15 THR A 310 ASN A 318 1 9 HELIX 16 16 LYS A 330 THR A 335 1 6 HELIX 17 17 THR A 361 LYS A 365 5 5 HELIX 18 18 SER A 369 LYS A 383 1 15 HELIX 19 19 ALA A 394 HIS A 401 1 8 HELIX 20 20 MET A 404 MET A 429 1 26 HELIX 21 21 ARG A 477 GLY A 479 5 3 HELIX 22 22 ASP A 480 ASN A 490 1 11 SHEET 1 A 7 THR A 42 ILE A 45 0 SHEET 2 A 7 VAL A 461 VAL A 465 -1 O VAL A 461 N ILE A 45 SHEET 3 A 7 TYR A 432 THR A 436 -1 N ILE A 435 O ILE A 464 SHEET 4 A 7 THR A 6 LEU A 11 1 N LEU A 11 O THR A 436 SHEET 5 A 7 LEU A 388 PHE A 393 1 O LEU A 391 N ILE A 10 SHEET 6 A 7 GLN A 322 GLU A 327 1 N LEU A 323 O ILE A 390 SHEET 7 A 7 GLU A 349 ILE A 354 1 O ARG A 350 N GLN A 322 SHEET 1 B 8 THR A 212 TYR A 213 0 SHEET 2 B 8 PHE A 236 VAL A 238 1 O ILE A 237 N TYR A 213 SHEET 3 B 8 GLN A 178 GLY A 184 -1 N VAL A 182 O PHE A 236 SHEET 4 B 8 VAL A 144 LEU A 150 1 N VAL A 146 O GLN A 178 SHEET 5 B 8 LEU A 111 LEU A 116 1 N ILE A 113 O HIS A 147 SHEET 6 B 8 ALA A 250 PHE A 253 1 O ALA A 250 N HIS A 112 SHEET 7 B 8 PHE A 285 THR A 288 1 O ALA A 287 N VAL A 251 SHEET 8 B 8 ALA A 299 ILE A 300 1 O ALA A 299 N TYR A 286 LINK OD1 ASP A 12 MN MN A 602 1555 1555 1.87 LINK OG SER A 62 MN MN A 602 1555 1555 1.94 LINK OD1 ASP A 397 MN MN A 601 1555 1555 2.13 LINK NE2 HIS A 401 MN MN A 601 1555 1555 2.22 LINK OD1 ASP A 438 MN MN A 602 1555 1555 1.97 LINK NE2 HIS A 439 MN MN A 602 1555 1555 2.07 LINK NE2 HIS A 456 MN MN A 601 1555 1555 2.37 LINK MN MN A 601 O HOH A 701 1555 1555 2.20 LINK MN MN A 601 O HOH A 702 1555 1555 2.09 LINK MN MN A 601 O HOH A 703 1555 1555 2.14 SITE 1 AC1 6 ASP A 397 HIS A 401 HIS A 456 HOH A 701 SITE 2 AC1 6 HOH A 702 HOH A 703 SITE 1 AC2 4 ASP A 12 SER A 62 ASP A 438 HIS A 439 SITE 1 AC3 8 HIS A 123 ARG A 153 ASP A 154 ARG A 185 SITE 2 AC3 8 ARG A 191 ARG A 257 ASP A 259 ARG A 260 CRYST1 72.802 80.689 89.254 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013736 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012393 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011204 0.00000