HEADER OXIDOREDUCTASE 15-AUG-07 2QYT TITLE CRYSTAL STRUCTURE OF 2-DEHYDROPANTOATE 2-REDUCTASE FROM PORPHYROMONAS TITLE 2 GINGIVALIS W83 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-DEHYDROPANTOATE 2-REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS; SOURCE 3 ORGANISM_TAXID: 242619; SOURCE 4 STRAIN: W83; SOURCE 5 ATCC: BAA-308; SOURCE 6 GENE: PANE, PG_2205; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS APC81190, 2-DEHYDROPANTOATE 2-REDUCTASE, PORPHYROMONAS GINGIVALIS KEYWDS 2 W83, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,R.WU,S.MOY,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL GENOMICS AUTHOR 2 (MCSG) REVDAT 3 13-JUL-11 2QYT 1 VERSN REVDAT 2 24-FEB-09 2QYT 1 VERSN REVDAT 1 04-SEP-07 2QYT 0 JRNL AUTH K.TAN,R.WU,S.MOY,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF 2-DEHYDROPANTOATE 2-REDUCTASE FROM JRNL TITL 2 PORPHYROMONAS GINGIVALIS W83. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 16055 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 866 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 823 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2241 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 24.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.94000 REMARK 3 B22 (A**2) : -0.94000 REMARK 3 B33 (A**2) : 1.87000 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): 0.274 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.231 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.152 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.355 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2357 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3193 ; 1.748 ; 2.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 295 ; 6.688 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 100 ;32.654 ;22.700 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 409 ;19.520 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;19.216 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 360 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1741 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1176 ; 0.232 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1598 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 137 ; 0.175 ; 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): 64 ; 0.257 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.165 ; 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): 1489 ; 0.966 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2324 ; 1.486 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 991 ; 2.196 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 864 ; 3.288 ; 4.500 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 : 2 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 4 A 189 REMARK 3 ORIGIN FOR THE GROUP (A): 40.8870 21.3250 35.7410 REMARK 3 T TENSOR REMARK 3 T11: -0.1434 T22: -0.1499 REMARK 3 T33: -0.3167 T12: -0.0149 REMARK 3 T13: 0.0009 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 2.6513 L22: 1.0355 REMARK 3 L33: 1.9008 L12: -0.6739 REMARK 3 L13: -1.1241 L23: -0.0517 REMARK 3 S TENSOR REMARK 3 S11: -0.0029 S12: 0.0292 S13: 0.0289 REMARK 3 S21: 0.0518 S22: 0.0498 S23: 0.0844 REMARK 3 S31: -0.1504 S32: -0.0694 S33: -0.0469 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 190 A 260 REMARK 3 RESIDUE RANGE : A 281 A 310 REMARK 3 ORIGIN FOR THE GROUP (A): 25.0250 21.8310 12.7870 REMARK 3 T TENSOR REMARK 3 T11: 0.0350 T22: 0.3585 REMARK 3 T33: 0.0052 T12: -0.0660 REMARK 3 T13: 0.0129 T23: 0.0664 REMARK 3 L TENSOR REMARK 3 L11: 6.3784 L22: 7.0298 REMARK 3 L33: 16.7711 L12: 2.4181 REMARK 3 L13: 8.1315 L23: 5.6380 REMARK 3 S TENSOR REMARK 3 S11: -0.0658 S12: 0.1653 S13: -0.4713 REMARK 3 S21: -0.3506 S22: 0.0614 S23: 0.4173 REMARK 3 S31: -0.0611 S32: -0.6691 S33: 0.0045 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2QYT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-07. REMARK 100 THE RCSB ID CODE IS RCSB044215. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97925, 0.97938 REMARK 200 MONOCHROMATOR : SI 111 CRYSTAL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16966 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 62.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.47500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE, HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M MES, 30% REMARK 280 PEG MME5000, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 49.13000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.78850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.78850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.56500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.78850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.78850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 73.69500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.78850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.78850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.56500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.78850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.78850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 73.69500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.13000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY REMARK 300 INFORMATION FOR THE STRUCTURE IN THIS ENTRY. REMARK 300 AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS REMARK 300 PROTEIN IS EXPERIMENTALLY UNKNOWN. 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MSE A 1 REMARK 465 ASN A 2 REMARK 465 GLN A 3 REMARK 465 PRO A 261 REMARK 465 PRO A 262 REMARK 465 GLU A 263 REMARK 465 SER A 264 REMARK 465 THR A 265 REMARK 465 SER A 266 REMARK 465 SER A 267 REMARK 465 MSE A 268 REMARK 465 HIS A 269 REMARK 465 SER A 270 REMARK 465 ASP A 271 REMARK 465 PHE A 272 REMARK 465 LEU A 273 REMARK 465 GLN A 274 REMARK 465 GLY A 275 REMARK 465 GLY A 276 REMARK 465 SER A 277 REMARK 465 THR A 278 REMARK 465 GLU A 279 REMARK 465 VAL A 280 REMARK 465 ARG A 311 REMARK 465 THR A 312 REMARK 465 ALA A 313 REMARK 465 ASN A 314 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 GLU A 292 CD GLU A 292 OE2 0.086 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 50 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 50 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 PRO A 246 C - N - CA ANGL. DEV. = 10.9 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 LEU A 13 52.87 -110.72 REMARK 500 ASP A 32 79.00 -102.10 REMARK 500 ASP A 118 33.44 -146.74 REMARK 500 SER A 140 79.65 -108.39 REMARK 500 GLN A 244 -89.91 -115.25 REMARK 500 VAL A 245 93.40 64.30 REMARK 500 PRO A 246 -152.22 -19.73 REMARK 500 THR A 284 -58.40 -124.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ARG A 295 24.3 L L OUTSIDE RANGE 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 SO4 A 315 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 316 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 317 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 318 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 319 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 320 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 321 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 322 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 323 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 324 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC81190 RELATED DB: TARGETDB DBREF 2QYT A 1 314 UNP Q7MT04 Q7MT04_PORGI 1 314 SEQADV 2QYT SER A -2 UNP Q7MT04 EXPRESSION TAG SEQADV 2QYT ASN A -1 UNP Q7MT04 EXPRESSION TAG SEQADV 2QYT ALA A 0 UNP Q7MT04 EXPRESSION TAG SEQRES 1 A 317 SER ASN ALA MSE ASN GLN GLN PRO ILE LYS ILE ALA VAL SEQRES 2 A 317 PHE GLY LEU GLY GLY VAL GLY GLY TYR TYR GLY ALA MSE SEQRES 3 A 317 LEU ALA LEU ARG ALA ALA ALA THR ASP GLY LEU LEU GLU SEQRES 4 A 317 VAL SER TRP ILE ALA ARG GLY ALA HIS LEU GLU ALA ILE SEQRES 5 A 317 ARG ALA ALA GLY GLY LEU ARG VAL VAL THR PRO SER ARG SEQRES 6 A 317 ASP PHE LEU ALA ARG PRO THR CYS VAL THR ASP ASN PRO SEQRES 7 A 317 ALA GLU VAL GLY THR VAL ASP TYR ILE LEU PHE CYS THR SEQRES 8 A 317 LYS ASP TYR ASP MSE GLU ARG GLY VAL ALA GLU ILE ARG SEQRES 9 A 317 PRO MSE ILE GLY GLN ASN THR LYS ILE LEU PRO LEU LEU SEQRES 10 A 317 ASN GLY ALA ASP ILE ALA GLU ARG MSE ARG THR TYR LEU SEQRES 11 A 317 PRO ASP THR VAL VAL TRP LYS GLY CYS VAL TYR ILE SER SEQRES 12 A 317 ALA ARG LYS SER ALA PRO GLY LEU ILE THR LEU GLU ALA SEQRES 13 A 317 ASP ARG GLU LEU PHE TYR PHE GLY SER GLY LEU PRO GLU SEQRES 14 A 317 GLN THR ASP ASP GLU VAL ARG LEU ALA GLU LEU LEU THR SEQRES 15 A 317 ALA ALA GLY ILE ARG ALA TYR ASN PRO THR ASP ILE ASP SEQRES 16 A 317 TRP TYR ILE MSE LYS LYS PHE MSE MSE ILE SER VAL THR SEQRES 17 A 317 ALA THR ALA THR ALA TYR PHE ASP LYS PRO ILE GLY SER SEQRES 18 A 317 ILE LEU THR GLU HIS GLU PRO GLU LEU LEU SER LEU LEU SEQRES 19 A 317 GLU GLU VAL ALA GLU LEU PHE ARG ALA LYS TYR GLY GLN SEQRES 20 A 317 VAL PRO ASP ASP VAL VAL GLN GLN LEU LEU ASP LYS GLN SEQRES 21 A 317 ARG LYS MSE PRO PRO GLU SER THR SER SER MSE HIS SER SEQRES 22 A 317 ASP PHE LEU GLN GLY GLY SER THR GLU VAL GLU THR LEU SEQRES 23 A 317 THR GLY TYR VAL VAL ARG GLU ALA GLU ALA LEU ARG VAL SEQRES 24 A 317 ASP LEU PRO MSE TYR LYS ARG MSE TYR ARG GLU LEU VAL SEQRES 25 A 317 SER ARG THR ALA ASN MODRES 2QYT MSE A 23 MET SELENOMETHIONINE MODRES 2QYT MSE A 93 MET SELENOMETHIONINE MODRES 2QYT MSE A 103 MET SELENOMETHIONINE MODRES 2QYT MSE A 123 MET SELENOMETHIONINE MODRES 2QYT MSE A 196 MET SELENOMETHIONINE MODRES 2QYT MSE A 200 MET SELENOMETHIONINE MODRES 2QYT MSE A 201 MET SELENOMETHIONINE MODRES 2QYT MSE A 260 MET SELENOMETHIONINE MODRES 2QYT MSE A 300 MET SELENOMETHIONINE MODRES 2QYT MSE A 304 MET SELENOMETHIONINE HET MSE A 23 8 HET MSE A 93 8 HET MSE A 103 8 HET MSE A 123 8 HET MSE A 196 13 HET MSE A 200 8 HET MSE A 201 13 HET MSE A 260 8 HET MSE A 300 8 HET MSE A 304 8 HET SO4 A 315 5 HET SO4 A 316 5 HET SO4 A 317 5 HET SO4 A 318 5 HET SO4 A 319 5 HET EDO A 320 4 HET EDO A 321 4 HET EDO A 322 4 HET EDO A 323 4 HET EDO A 324 4 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 10(C5 H11 N O2 SE) FORMUL 2 SO4 5(O4 S 2-) FORMUL 7 EDO 5(C2 H6 O2) FORMUL 12 HOH *147(H2 O) HELIX 1 1 GLY A 14 THR A 31 1 18 HELIX 2 2 ARG A 42 GLY A 53 1 12 HELIX 3 3 ASN A 74 GLY A 79 1 6 HELIX 4 4 ASP A 92 ARG A 101 1 10 HELIX 5 5 ASP A 118 ARG A 124 1 7 HELIX 6 6 THR A 168 ALA A 181 1 14 HELIX 7 7 ASP A 190 ASP A 213 1 24 HELIX 8 8 PRO A 215 HIS A 223 1 9 HELIX 9 9 HIS A 223 TYR A 242 1 20 HELIX 10 10 ASP A 248 MSE A 260 1 13 HELIX 11 11 THR A 284 LEU A 294 1 11 HELIX 12 12 LEU A 298 GLU A 307 1 10 SHEET 1 A 5 CYS A 70 THR A 72 0 SHEET 2 A 5 LEU A 35 ILE A 40 1 N TRP A 39 O THR A 72 SHEET 3 A 5 ILE A 6 PHE A 11 1 N VAL A 10 O ILE A 40 SHEET 4 A 5 VAL A 81 PHE A 86 1 O LEU A 85 N ALA A 9 SHEET 5 A 5 ILE A 104 PRO A 112 1 O LEU A 111 N ILE A 84 SHEET 1 B 4 ASP A 63 ALA A 66 0 SHEET 2 B 4 LEU A 55 VAL A 58 -1 N LEU A 55 O ALA A 66 SHEET 3 B 4 LEU A 148 LEU A 151 1 O ILE A 149 N ARG A 56 SHEET 4 B 4 ALA A 141 ALA A 145 -1 N ARG A 142 O THR A 150 SHEET 1 C 3 LYS A 134 TYR A 138 0 SHEET 2 C 3 LEU A 157 GLY A 161 -1 O GLY A 161 N LYS A 134 SHEET 3 C 3 ALA A 185 TYR A 186 1 O TYR A 186 N PHE A 158 LINK C ALA A 22 N MSE A 23 1555 1555 1.33 LINK C MSE A 23 N LEU A 24 1555 1555 1.33 LINK C ASP A 92 N MSE A 93 1555 1555 1.33 LINK C MSE A 93 N GLU A 94 1555 1555 1.33 LINK C PRO A 102 N MSE A 103 1555 1555 1.33 LINK C MSE A 103 N ILE A 104 1555 1555 1.33 LINK C ARG A 122 N MSE A 123 1555 1555 1.33 LINK C MSE A 123 N ARG A 124 1555 1555 1.33 LINK C ILE A 195 N MSE A 196 1555 1555 1.33 LINK C MSE A 196 N LYS A 197 1555 1555 1.33 LINK C PHE A 199 N MSE A 200 1555 1555 1.33 LINK C MSE A 200 N MSE A 201 1555 1555 1.34 LINK C MSE A 201 N ILE A 202 1555 1555 1.33 LINK C LYS A 259 N MSE A 260 1555 1555 1.35 LINK C PRO A 299 N MSE A 300 1555 1555 1.33 LINK C MSE A 300 N TYR A 301 1555 1555 1.34 LINK C ARG A 303 N MSE A 304 1555 1555 1.33 LINK C MSE A 304 N TYR A 305 1555 1555 1.33 SITE 1 AC1 9 GLY A 15 LYS A 89 ALA A 141 ARG A 142 SITE 2 AC1 9 LYS A 143 SO4 A 318 EDO A 320 HOH A 443 SITE 3 AC1 9 HOH A 444 SITE 1 AC2 8 LEU A 13 ALA A 41 ARG A 42 HIS A 45 SITE 2 AC2 8 LYS A 143 SO4 A 318 HOH A 365 HOH A 393 SITE 1 AC3 6 ASP A 32 GLU A 281 THR A 282 GLY A 285 SITE 2 AC3 6 ARG A 289 TYR A 305 SITE 1 AC4 10 GLY A 12 LEU A 13 GLY A 14 CYS A 87 SITE 2 AC4 10 THR A 88 ASP A 90 SO4 A 315 SO4 A 316 SITE 3 AC4 10 EDO A 320 HOH A 443 SITE 1 AC5 4 TYR A 186 ASN A 187 EDO A 324 HOH A 459 SITE 1 AC6 8 GLY A 12 GLY A 14 GLY A 15 VAL A 16 SITE 2 AC6 8 GLY A 17 CYS A 87 SO4 A 315 SO4 A 318 SITE 1 AC7 4 THR A 80 GLY A 105 GLN A 106 THR A 130 SITE 1 AC8 3 ALA A 293 ARG A 295 HOH A 440 SITE 1 AC9 6 TYR A 19 ARG A 62 ASP A 154 GLU A 156 SITE 2 AC9 6 ARG A 184 HOH A 471 SITE 1 BC1 5 TYR A 186 ASN A 187 PRO A 188 TYR A 194 SITE 2 BC1 5 SO4 A 319 CRYST1 79.577 79.577 98.260 90.00 90.00 90.00 P 41 21 2 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 0.012566 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012566 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010177 0.00000