HEADER HYDROLASE 23-APR-18 6GDF TITLE DIHYDROOROTASE FROM AQUIFEX AEOLICUS UNDER 600 BAR OF HYDROSTATIC TITLE 2 PRESSURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DHOASE; COMPND 5 EC: 3.5.2.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 224324; SOURCE 4 STRAIN: VF5; SOURCE 5 GENE: PYRC, AQ_806; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DIHYDROOROTASE, AQUIFEX AEOLICUS, AT 600 BAR HYDROSTATIC PRESSURE, KEYWDS 2 ROOM TEMPERATURE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.PRANGE,E.GIRARD,G.HERVE,D.R.EVANS REVDAT 4 17-JAN-24 6GDF 1 REMARK REVDAT 3 27-MAR-19 6GDF 1 JRNL REVDAT 2 20-FEB-19 6GDF 1 REMARK LINK REVDAT 1 30-JAN-19 6GDF 0 JRNL AUTH T.PRANGE,E.GIRARD,R.FOURME,A.C.DHAUSSY,B.EDWARDS,A.VAISHNAV, JRNL AUTH 2 C.PATEL,H.GUY-EVANS,G.HERVE,D.R.EVANS JRNL TITL PRESSURE-INDUCED ACTIVATION OF LATENT DIHYDROOROTASE FROM JRNL TITL 2 AQUIFEX AEOLICUS AS REVEALED BY HIGH PRESSURE PROTEIN JRNL TITL 3 CRYSTALLOGRAPHY. JRNL REF FEBS J. V. 286 1204 2019 JRNL REFN ISSN 1742-464X JRNL PMID 30657257 JRNL DOI 10.1111/FEBS.14758 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.HERVE,H.GUY-EVANS,R.FERNADO,C.PATEL,F.HACHEM,D.R.EVANS REMARK 1 TITL ACTIVATION OF LATENT DIHYDROOROTASE FROM AQUIFEX AEOLICUS BY REMARK 1 TITL 2 PRESSURE REMARK 1 REF J. BIOL. CHEM. V. 292 629 2017 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 27746403 REMARK 1 DOI 10.1074/JBC.M116.739862 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 69.8 REMARK 3 NUMBER OF REFLECTIONS : 13031 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NONE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 863 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.3560 REMARK 3 BIN FREE R VALUE SET COUNT : 0 REMARK 3 BIN FREE R VALUE : 0.0000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2847 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : 0.06000 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): 0.717 REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.128 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.304 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2893 ; 0.010 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3905 ; 1.338 ; 1.756 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 364 ; 9.062 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;35.641 ;22.277 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 496 ;21.987 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;21.746 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 401 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2061 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1468 ; 5.038 ; 4.234 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1828 ; 7.346 ; 6.299 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1425 ; 6.199 ; 4.754 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): 4325 ;11.357 ;58.932 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6GDF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009773. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID27 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.3738 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14277 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 45.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 76.8 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.13500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.83300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BUCCANEER REMARK 200 STARTING MODEL: 1XRF REMARK 200 REMARK 200 REMARK: PRISM, 0.2 MM REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ETHANOL (12%), PEG 400 (4%), ACETATE, REMARK 280 PH 4.6 (0.1 M), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 32.75900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.75900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 45.42000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 88.24400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.42000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 88.24400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.75900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.42000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 88.24400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.75900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.42000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 88.24400 REMARK 290 SMTRY3 8 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 TOTAL BURIED SURFACE AREA: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 ASP A 183 REMARK 465 ASP A 184 REMARK 465 LYS A 185 REMARK 465 LEU A 186 REMARK 465 ALA A 187 REMARK 465 TYR A 188 REMARK 465 GLY A 189 REMARK 465 VAL A 190 REMARK 465 ILE A 191 REMARK 465 ASN A 192 REMARK 465 GLU A 193 REMARK 465 GLY A 194 REMARK 465 GLU A 195 REMARK 465 VAL A 196 REMARK 465 SER A 197 REMARK 465 ALA A 198 REMARK 465 LEU A 199 REMARK 465 LEU A 200 REMARK 465 GLY A 201 REMARK 465 LEU A 202 REMARK 465 SER A 203 REMARK 465 SER A 204 REMARK 465 ARG A 205 REMARK 465 ALA A 206 REMARK 465 PRO A 207 REMARK 465 PHE A 263 REMARK 465 THR A 264 REMARK 465 GLU A 265 REMARK 465 ARG A 266 REMARK 465 GLU A 267 REMARK 465 VAL A 268 REMARK 465 LEU A 269 REMARK 465 ASN A 270 REMARK 465 SER A 271 REMARK 465 GLY A 272 REMARK 465 ALA A 273 REMARK 465 ASN A 274 REMARK 465 ALA A 275 REMARK 465 ARG A 276 REMARK 465 VAL A 277 REMARK 465 ASN A 278 REMARK 465 PRO A 279 REMARK 465 PRO A 280 REMARK 465 LEU A 281 REMARK 465 ARG A 282 REMARK 465 LYS A 283 REMARK 465 LYS A 284 REMARK 465 GLU A 285 REMARK 465 LYS A 314 REMARK 465 GLU A 315 REMARK 465 LEU A 316 REMARK 465 VAL A 317 REMARK 465 GLU A 318 REMARK 465 PHE A 319 REMARK 465 ALA A 320 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 N ASP A 286 O HOH A 601 2.13 REMARK 500 NH1 ARG A 80 O HOH A 602 2.16 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 OE2 GLU A 208 NH1 ARG A 223 4556 1.21 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 A 156 C - N - CA ANGL. DEV. = 12.9 DEGREES REMARK 500 PRO A 156 CA - N - CD ANGL. DEV. = -12.1 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 ASN A 8 10.73 87.24 REMARK 500 ASN A 37 73.10 50.90 REMARK 500 HIS A 61 87.39 -150.68 REMARK 500 GLU A 73 159.77 169.33 REMARK 500 ASN A 95 43.63 -83.13 REMARK 500 LEU A 118 -70.55 -99.82 REMARK 500 ASP A 153 81.55 8.20 REMARK 500 SER A 155 -11.61 -157.04 REMARK 500 PRO A 156 134.53 4.43 REMARK 500 VAL A 157 98.69 -54.36 REMARK 500 ASP A 159 98.22 -43.50 REMARK 500 HIS A 180 149.60 78.85 REMARK 500 CYS A 181 -88.36 175.22 REMARK 500 ARG A 287 -32.04 -30.75 REMARK 500 PHE A 312 -50.18 -135.96 REMARK 500 THR A 353 -84.04 -120.60 REMARK 500 ASP A 415 29.48 41.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TRP A 0 MET A 1 147.87 REMARK 500 LYS A 7 ASN A 8 147.98 REMARK 500 LEU A 261 LEU A 262 148.04 REMARK 500 GLY A 323 ILE A 324 -147.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 164 0.10 SIDE CHAIN REMARK 500 ARG A 223 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 687 DISTANCE = 6.11 ANGSTROMS 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 ZN A 500 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 61 NE2 REMARK 620 2 HIS A 63 NE2 108.0 REMARK 620 3 CYS A 181 SG 117.4 133.8 REMARK 620 4 ASP A 305 OD1 61.0 93.6 100.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XRF RELATED DB: PDB REMARK 900 SAME AT CRYO (100K), P. AMBIENT REMARK 900 RELATED ID: 1XRT RELATED DB: PDB DBREF 6GDF A 1 422 UNP O66990 PYRC_AQUAE 1 422 SEQADV 6GDF TRP A 0 UNP O66990 EXPRESSION TAG SEQRES 1 A 423 TRP MET LEU LYS LEU ILE VAL LYS ASN GLY TYR VAL ILE SEQRES 2 A 423 ASP PRO SER GLN ASN LEU GLU GLY GLU PHE ASP ILE LEU SEQRES 3 A 423 VAL GLU ASN GLY LYS ILE LYS LYS ILE ASP LYS ASN ILE SEQRES 4 A 423 LEU VAL PRO GLU ALA GLU ILE ILE ASP ALA LYS GLY LEU SEQRES 5 A 423 ILE VAL CYS PRO GLY PHE ILE ASP ILE HIS VAL HIS LEU SEQRES 6 A 423 ARG ASP PRO GLY GLN THR TYR LYS GLU ASP ILE GLU SER SEQRES 7 A 423 GLY SER ARG CYS ALA VAL ALA GLY GLY PHE THR THR ILE SEQRES 8 A 423 VAL CYS MET PRO ASN THR ASN PRO PRO ILE ASP ASN THR SEQRES 9 A 423 THR VAL VAL ASN TYR ILE LEU GLN LYS SER LYS SER VAL SEQRES 10 A 423 GLY LEU CYS ARG VAL LEU PRO THR GLY THR ILE THR LYS SEQRES 11 A 423 GLY ARG LYS GLY LYS GLU ILE ALA ASP PHE TYR SER LEU SEQRES 12 A 423 LYS GLU ALA GLY CYS VAL ALA PHE THR ASP ASP GLY SER SEQRES 13 A 423 PRO VAL MET ASP SER SER VAL MET ARG LYS ALA LEU GLU SEQRES 14 A 423 LEU ALA SER GLN LEU GLY VAL PRO ILE MET ASP HIS CYS SEQRES 15 A 423 GLU ASP ASP LYS LEU ALA TYR GLY VAL ILE ASN GLU GLY SEQRES 16 A 423 GLU VAL SER ALA LEU LEU GLY LEU SER SER ARG ALA PRO SEQRES 17 A 423 GLU ALA GLU GLU ILE GLN ILE ALA ARG ASP GLY ILE LEU SEQRES 18 A 423 ALA GLN ARG THR GLY GLY HIS VAL HIS ILE GLN HIS VAL SEQRES 19 A 423 SER THR LYS LEU SER LEU GLU ILE ILE GLU PHE PHE LYS SEQRES 20 A 423 GLU LYS GLY VAL LYS ILE THR CYS GLU VAL ASN PRO ASN SEQRES 21 A 423 HIS LEU LEU PHE THR GLU ARG GLU VAL LEU ASN SER GLY SEQRES 22 A 423 ALA ASN ALA ARG VAL ASN PRO PRO LEU ARG LYS LYS GLU SEQRES 23 A 423 ASP ARG LEU ALA LEU ILE GLU GLY VAL LYS ARG GLY ILE SEQRES 24 A 423 ILE ASP CYS PHE ALA THR ASP HIS ALA PRO HIS GLN THR SEQRES 25 A 423 PHE GLU LYS GLU LEU VAL GLU PHE ALA MET PRO GLY ILE SEQRES 26 A 423 ILE GLY LEU GLN THR ALA LEU PRO SER ALA LEU GLU LEU SEQRES 27 A 423 TYR ARG LYS GLY ILE ILE SER LEU LYS LYS LEU ILE GLU SEQRES 28 A 423 MET PHE THR ILE ASN PRO ALA ARG ILE ILE GLY VAL ASP SEQRES 29 A 423 LEU GLY THR LEU LYS LEU GLY SER PRO ALA ASP ILE THR SEQRES 30 A 423 ILE PHE ASP PRO ASN LYS GLU TRP ILE LEU ASN GLU GLU SEQRES 31 A 423 THR ASN LEU SER LYS SER ARG ASN THR PRO LEU TRP GLY SEQRES 32 A 423 LYS VAL LEU LYS GLY LYS VAL ILE TYR THR ILE LYS ASP SEQRES 33 A 423 GLY LYS MET VAL TYR LYS ASP HET ZN A 500 1 HET SO4 A 501 5 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 2 ZN ZN 2+ FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *87(H2 O) HELIX 1 AA1 PRO A 14 ASN A 17 5 4 HELIX 2 AA2 ASP A 74 GLY A 85 1 12 HELIX 3 AA3 ASN A 102 GLY A 117 1 16 HELIX 4 AA4 THR A 128 LYS A 132 5 5 HELIX 5 AA5 ASP A 138 GLY A 146 1 9 HELIX 6 AA6 ASP A 159 GLY A 174 1 16 HELIX 7 AA7 ALA A 209 GLY A 225 1 17 HELIX 8 AA8 THR A 235 LYS A 248 1 14 HELIX 9 AA9 ARG A 287 ARG A 296 1 10 HELIX 10 AB1 THR A 329 LYS A 340 1 12 HELIX 11 AB2 SER A 344 MET A 351 1 8 HELIX 12 AB3 THR A 353 ILE A 360 1 8 SHEET 1 AA1 4 LYS A 30 ASP A 35 0 SHEET 2 AA1 4 LEU A 18 GLU A 27 -1 N LEU A 25 O LYS A 33 SHEET 3 AA1 4 LYS A 3 ASP A 13 -1 N ASP A 13 O LEU A 18 SHEET 4 AA1 4 GLU A 44 ASP A 47 1 O GLU A 44 N ILE A 5 SHEET 1 AA2 7 LYS A 30 ASP A 35 0 SHEET 2 AA2 7 LEU A 18 GLU A 27 -1 N LEU A 25 O LYS A 33 SHEET 3 AA2 7 LYS A 3 ASP A 13 -1 N ASP A 13 O LEU A 18 SHEET 4 AA2 7 ILE A 52 PRO A 55 1 O VAL A 53 N TYR A 10 SHEET 5 AA2 7 ILE A 375 ILE A 385 -1 O PHE A 378 N ILE A 52 SHEET 6 AA2 7 VAL A 404 LYS A 414 -1 O ILE A 413 N ILE A 375 SHEET 7 AA2 7 LYS A 417 LYS A 421 -1 O VAL A 419 N THR A 412 SHEET 1 AA3 3 PHE A 57 VAL A 62 0 SHEET 2 AA3 3 PHE A 87 CYS A 92 1 O VAL A 91 N ASP A 59 SHEET 3 AA3 3 ARG A 120 PRO A 123 1 O ARG A 120 N THR A 88 SHEET 1 AA4 4 ILE A 177 ASP A 179 0 SHEET 2 AA4 4 VAL A 228 ILE A 230 1 O HIS A 229 N ILE A 177 SHEET 3 AA4 4 ILE A 252 VAL A 256 1 O THR A 253 N ILE A 230 SHEET 4 AA4 4 CYS A 301 PHE A 302 1 O CYS A 301 N VAL A 256 LINK NE2 HIS A 61 ZN ZN A 500 1555 1555 2.04 LINK NE2 HIS A 63 ZN ZN A 500 1555 1555 2.03 LINK SG CYS A 181 ZN ZN A 500 1555 1555 2.68 LINK OD1 ASP A 305 ZN ZN A 500 1555 1555 2.65 CISPEP 1 ASP A 66 PRO A 67 0 -0.47 CISPEP 2 ASN A 97 PRO A 98 0 7.07 CISPEP 3 MET A 321 PRO A 322 0 -20.89 SITE 1 AC1 5 HIS A 61 HIS A 63 ASP A 153 CYS A 181 SITE 2 AC1 5 ASP A 305 SITE 1 AC2 2 GLN A 310 THR A 311 CRYST1 90.840 176.488 65.518 90.00 90.00 90.00 C 2 2 21 8 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 0.011008 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005666 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015263 0.00000