HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 06-MAR-08 3CGV OBSLTE 27-OCT-10 3CGV 3OZ2 TITLE CRYSTAL STRUCTURE OF GERANYLGERANYL BACTERIOCHLOROPHYLL REDUCTASE-LIKE TITLE 2 FIXC HOMOLOG (NP_393992.1) FROM THERMOPLASMA ACIDOPHILUM AT 1.60 A TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GERANYLGERANYL REDUCTASE RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOPLASMA ACIDOPHILUM DSM 1728; SOURCE 3 ORGANISM_TAXID: 273075; SOURCE 4 STRAIN: DSM 1728 / AMRC-C165 / IFO 15155 / JCM 9062; SOURCE 5 ATCC: 25905; SOURCE 6 GENE: NP_393992.1, TA0516; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS NP_393992.1, GERANYLGERANYL BACTERIOCHLOROPHYLL REDUCTASE-LIKE FIXC KEYWDS 2 HOMOLOG, FAD BINDING DOMAIN, STRUCTURAL GENOMICS, JOINT CENTER FOR KEYWDS 3 STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, KEYWDS 4 UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 3 27-OCT-10 3CGV 1 OBSLTE REVDAT 2 24-FEB-09 3CGV 1 VERSN REVDAT 1 18-MAR-08 3CGV 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF GERANYLGERANYL BACTERIOCHLOROPHYLL JRNL TITL 2 REDUCTASE-LIKE FIXC HOMOLOG (NP_393992.1) FROM THERMOPLASMA JRNL TITL 3 ACIDOPHILUM AT 1.60 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0067 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 55126 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2799 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3822 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 203 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2853 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 139 REMARK 3 SOLVENT ATOMS : 308 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.45000 REMARK 3 B22 (A**2) : 0.95000 REMARK 3 B33 (A**2) : -0.50000 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): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.078 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.696 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3112 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2121 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4217 ; 1.682 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5209 ; 1.422 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 413 ; 6.462 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;36.316 ;24.561 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 527 ;12.855 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;16.461 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 475 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3425 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 578 ; 0.002 ; 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): 1944 ; 0.804 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 803 ; 0.251 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3126 ; 1.381 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1168 ; 2.450 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1076 ; 3.809 ; 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 : 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 0 A 382 REMARK 3 ORIGIN FOR THE GROUP (A): 13.8305 49.1354 24.7827 REMARK 3 T TENSOR REMARK 3 T11: -0.1321 T22: -0.1290 REMARK 3 T33: -0.1265 T12: 0.0031 REMARK 3 T13: 0.0033 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 1.1348 L22: 0.9566 REMARK 3 L33: 1.6729 L12: -0.1697 REMARK 3 L13: 0.6078 L23: -0.6855 REMARK 3 S TENSOR REMARK 3 S11: -0.0456 S12: -0.1643 S13: 0.0243 REMARK 3 S21: 0.2238 S22: 0.0038 S23: -0.0518 REMARK 3 S31: -0.0509 S32: -0.0267 S33: 0.0418 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: REMARK 3 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY REMARK 3 OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 REMARK 3 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. REMARK 3 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. REMARK 3 4. FAD IS MODELED BASED ON DENSITY. REMARK 3 5. AN UNKNOWN LIGAND (UNL), BASED ON THE PROPOSED FUNCTION, IS REMARK 3 MODELED AND MAY BE RELATED TO GERANYLGERANYL-DIPHOSPHATE. REMARK 3 6. EDO AND IPA ARE MODELED BASED ON CRYSTALLIZATION CONDITIONS. REMARK 4 REMARK 4 3CGV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-08. REMARK 100 THE RCSB ID CODE IS RCSB046760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91837, 0.97920, 0.97862 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(111) BENT REMARK 200 (HORIZONTAL FOCUSING) REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55180 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 29.437 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : 0.43000 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: SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NANODROP, 15.0% GLYCEROL, 8.5% REMARK 280 ISOPROPANOL, 17.0% PEG 4000, 0.1M HEPES PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K 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 24.77250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.87400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.31100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.87400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.77250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.31100 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 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 87 REMARK 465 GLU A 88 REMARK 465 LYS A 89 REMARK 465 ALA A 90 REMARK 465 GLY A 91 REMARK 465 GLU A 387 REMARK 465 VAL A 388 REMARK 465 VAL A 389 REMARK 465 LYS A 390 REMARK 465 GLU A 391 REMARK 465 LEU A 392 REMARK 465 GLU A 393 REMARK 465 ASP A 394 REMARK 465 LEU A 395 REMARK 465 ILE A 396 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 LYS A 50 CG CD CE NZ REMARK 470 LYS A 59 CD CE NZ REMARK 470 ARG A 62 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 68 CD OE1 OE2 REMARK 470 LYS A 80 CG CD CE NZ REMARK 470 ASN A 92 CG OD1 ND2 REMARK 470 GLU A 93 CG CD OE1 OE2 REMARK 470 LYS A 102 CD CE NZ REMARK 470 LYS A 121 CE NZ REMARK 470 HIS A 232 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 234 CZ NH1 NH2 REMARK 470 GLU A 246 CD OE1 OE2 REMARK 470 LYS A 252 CE NZ REMARK 470 GLN A 322 CG CD OE1 NE2 REMARK 470 ARG A 337 CD NE CZ NH1 NH2 REMARK 470 LYS A 348 CD CE NZ REMARK 470 LYS A 359 CG CD CE NZ REMARK 470 LEU A 360 CD1 CD2 REMARK 470 GLN A 367 CG CD OE1 NE2 REMARK 470 LYS A 379 CG CD CE NZ REMARK 470 GLU A 383 CG CD OE1 OE2 REMARK 470 LYS A 384 CE NZ REMARK 470 TYR A 385 CG CD1 CD2 CE1 CE2 CZ OH 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 MSE A 187 CB MSE A 187 CG 0.229 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 ASP A 101 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 MSE A 187 CG - SE - CE ANGL. DEV. = -13.7 DEGREES REMARK 500 ILE A 231 CG1 - CB - CG2 ANGL. DEV. = -14.2 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 ALA A 205 77.56 -152.06 REMARK 500 TYR A 385 52.76 -149.21 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 LEU A 98 GLU A 99 149.89 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 FAD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A 417 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 382454 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE. REMARK 999 2. THERE IS A DIFFERENCE IN ANNOTATION OF THE SEQUENCE OF REMARK 999 THIS PROTEIN BETWEEN UNIPROT AND GENBANK. THE N-TERMINAL REMARK 999 RESIDUES METYDVLV ARE LISTED IN GENBANK SEQUENCE NP_393992.1 REMARK 999 WHILE ONLY RESIDUE M IS LISTED IN UNIPROT SEQUENCE REMARK 999 AT POSITION 1. DBREF 3CGV A 9 396 UNP Q9HKS9 Q9HKS9_THEAC 2 389 SEQADV 3CGV GLY A 0 UNP Q9HKS9 LEADER SEQUENCE SEQADV 3CGV MSE A 1 UNP Q9HKS9 SEE REMARK 999 SEQADV 3CGV GLU A 2 UNP Q9HKS9 SEE REMARK 999 SEQADV 3CGV THR A 3 UNP Q9HKS9 SEE REMARK 999 SEQADV 3CGV TYR A 4 UNP Q9HKS9 SEE REMARK 999 SEQADV 3CGV ASP A 5 UNP Q9HKS9 SEE REMARK 999 SEQADV 3CGV VAL A 6 UNP Q9HKS9 SEE REMARK 999 SEQADV 3CGV LEU A 7 UNP Q9HKS9 SEE REMARK 999 SEQADV 3CGV VAL A 8 UNP Q9HKS9 SEE REMARK 999 SEQRES 1 A 397 GLY MSE GLU THR TYR ASP VAL LEU VAL VAL GLY GLY GLY SEQRES 2 A 397 PRO GLY GLY SER THR ALA ALA ARG TYR ALA ALA LYS TYR SEQRES 3 A 397 GLY LEU LYS THR LEU MSE ILE GLU LYS ARG PRO GLU ILE SEQRES 4 A 397 GLY SER PRO VAL ARG CYS GLY GLU GLY LEU SER LYS GLY SEQRES 5 A 397 ILE LEU ASN GLU ALA ASP ILE LYS ALA ASP ARG SER PHE SEQRES 6 A 397 ILE ALA ASN GLU VAL LYS GLY ALA ARG ILE TYR GLY PRO SEQRES 7 A 397 SER GLU LYS ARG PRO ILE ILE LEU GLN SER GLU LYS ALA SEQRES 8 A 397 GLY ASN GLU VAL GLY TYR VAL LEU GLU ARG ASP LYS PHE SEQRES 9 A 397 ASP LYS HIS LEU ALA ALA LEU ALA ALA LYS ALA GLY ALA SEQRES 10 A 397 ASP VAL TRP VAL LYS SER PRO ALA LEU GLY VAL ILE LYS SEQRES 11 A 397 GLU ASN GLY LYS VAL ALA GLY ALA LYS ILE ARG HIS ASN SEQRES 12 A 397 ASN GLU ILE VAL ASP VAL ARG ALA LYS MSE VAL ILE ALA SEQRES 13 A 397 ALA ASP GLY PHE GLU SER GLU PHE GLY ARG TRP ALA GLY SEQRES 14 A 397 LEU LYS SER VAL ILE LEU ALA ARG ASN ASP ILE ILE SER SEQRES 15 A 397 ALA LEU GLN TYR ARG MSE ILE ASN VAL ASP VAL ASP PRO SEQRES 16 A 397 ASP TYR THR ASP PHE TYR LEU GLY SER ILE ALA PRO ALA SEQRES 17 A 397 GLY TYR ILE TRP VAL PHE PRO LYS GLY GLU GLY MSE ALA SEQRES 18 A 397 ASN VAL GLY ILE GLY SER SER ILE ASN TRP ILE HIS ASN SEQRES 19 A 397 ARG PHE GLU LEU LYS ASN TYR LEU ASP ARG PHE ILE GLU SEQRES 20 A 397 ASN HIS PRO GLY LEU LYS LYS GLY GLN ASP ILE GLN LEU SEQRES 21 A 397 VAL THR GLY GLY VAL SER VAL SER LYS VAL LYS MSE PRO SEQRES 22 A 397 ILE THR MSE PRO GLY LEU MSE LEU VAL GLY ASP ALA ALA SEQRES 23 A 397 ARG LEU ILE ASP PRO ILE THR GLY GLY GLY ILE ALA ASN SEQRES 24 A 397 ALA ILE VAL SER GLY MSE TYR ALA ALA GLN VAL THR LYS SEQRES 25 A 397 GLU ALA ILE GLU SER ASN ASP TYR SER PRO GLN MSE MSE SEQRES 26 A 397 GLN LYS TYR GLU LYS LEU ILE LYS GLU ARG PHE GLU ARG SEQRES 27 A 397 LYS HIS LEU ARG ASN TRP VAL ALA LYS GLU LYS LEU ALA SEQRES 28 A 397 MSE LEU SER ASP ASP THR LEU ASP LYS LEU VAL ASP ILE SEQRES 29 A 397 VAL SER GLU GLN VAL LEU THR THR ILE SER VAL GLU ALA SEQRES 30 A 397 ILE LEU LYS ALA ILE ALA GLU LYS TYR PRO GLU VAL VAL SEQRES 31 A 397 LYS GLU LEU GLU ASP LEU ILE MODRES 3CGV MSE A 1 MET SELENOMETHIONINE MODRES 3CGV MSE A 31 MET SELENOMETHIONINE MODRES 3CGV MSE A 152 MET SELENOMETHIONINE MODRES 3CGV MSE A 187 MET SELENOMETHIONINE MODRES 3CGV MSE A 219 MET SELENOMETHIONINE MODRES 3CGV MSE A 271 MET SELENOMETHIONINE MODRES 3CGV MSE A 275 MET SELENOMETHIONINE MODRES 3CGV MSE A 279 MET SELENOMETHIONINE MODRES 3CGV MSE A 304 MET SELENOMETHIONINE MODRES 3CGV MSE A 323 MET SELENOMETHIONINE MODRES 3CGV MSE A 324 MET SELENOMETHIONINE MODRES 3CGV MSE A 351 MET SELENOMETHIONINE HET MSE A 1 13 HET MSE A 31 8 HET MSE A 152 8 HET MSE A 187 8 HET MSE A 219 13 HET MSE A 271 8 HET MSE A 275 13 HET MSE A 279 8 HET MSE A 304 13 HET MSE A 323 8 HET MSE A 324 8 HET MSE A 351 8 HET FAD A 401 53 HET UNL A 402 26 HET EDO A 403 4 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET EDO A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 4 HET EDO A 412 4 HET EDO A 413 4 HET EDO A 414 4 HET EDO A 415 4 HET EDO A 416 4 HET IPA A 417 4 HETNAM MSE SELENOMETHIONINE HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM UNL UNKNOWN LIGAND HETNAM EDO 1,2-ETHANEDIOL HETNAM IPA ISOPROPYL ALCOHOL HETSYN EDO ETHYLENE GLYCOL HETSYN IPA 2-PROPANOL FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 4 EDO 14(C2 H6 O2) FORMUL 18 IPA C3 H8 O FORMUL 19 HOH *308(H2 O) HELIX 1 1 GLY A 12 TYR A 25 1 14 HELIX 2 2 LYS A 50 ALA A 56 1 7 HELIX 3 3 GLU A 99 GLY A 115 1 17 HELIX 4 4 SER A 161 GLY A 168 1 8 HELIX 5 5 ALA A 175 ASN A 177 5 3 HELIX 6 6 ASN A 233 ASN A 247 1 15 HELIX 7 7 HIS A 248 LYS A 253 1 6 HELIX 8 8 GLY A 282 ARG A 286 5 5 HELIX 9 9 GLY A 295 ASN A 317 1 23 HELIX 10 10 SER A 320 ALA A 350 1 31 HELIX 11 11 SER A 353 SER A 365 1 13 HELIX 12 12 SER A 373 TYR A 385 1 13 SHEET 1 A 6 ASP A 117 TRP A 119 0 SHEET 2 A 6 THR A 29 ILE A 32 1 N THR A 29 O ASP A 117 SHEET 3 A 6 MSE A 1 VAL A 9 1 N VAL A 8 O LEU A 30 SHEET 4 A 6 GLU A 144 ALA A 155 1 O ILE A 154 N LEU A 7 SHEET 5 A 6 LYS A 133 HIS A 141 -1 N ILE A 139 O VAL A 146 SHEET 6 A 6 ALA A 124 GLU A 130 -1 N LEU A 125 O LYS A 138 SHEET 1 B 6 ASP A 117 TRP A 119 0 SHEET 2 B 6 THR A 29 ILE A 32 1 N THR A 29 O ASP A 117 SHEET 3 B 6 MSE A 1 VAL A 9 1 N VAL A 8 O LEU A 30 SHEET 4 B 6 GLU A 144 ALA A 155 1 O ILE A 154 N LEU A 7 SHEET 5 B 6 LEU A 278 LEU A 280 1 O MSE A 279 N ALA A 155 SHEET 6 B 6 THR A 274 MSE A 275 -1 N MSE A 275 O LEU A 278 SHEET 1 C 3 GLY A 47 SER A 49 0 SHEET 2 C 3 GLY A 95 LEU A 98 -1 O TYR A 96 N LEU A 48 SHEET 3 C 3 ILE A 65 VAL A 69 -1 N ASN A 67 O VAL A 97 SHEET 1 D 7 ILE A 83 LEU A 85 0 SHEET 2 D 7 GLY A 71 TYR A 75 -1 N ILE A 74 O ILE A 83 SHEET 3 D 7 TYR A 196 TYR A 200 1 O PHE A 199 N TYR A 75 SHEET 4 D 7 GLY A 208 GLY A 216 -1 O ILE A 210 N TYR A 200 SHEET 5 D 7 MSE A 219 SER A 227 -1 O ASN A 221 N PHE A 213 SHEET 6 D 7 ILE A 179 ILE A 188 -1 N TYR A 185 O VAL A 222 SHEET 7 D 7 GLN A 255 SER A 265 -1 O GLN A 255 N ILE A 188 LINK C GLY A 0 N MSE A 1 1555 1555 1.34 LINK C MSE A 1 N GLU A 2 1555 1555 1.34 LINK C LEU A 30 N MSE A 31 1555 1555 1.33 LINK C MSE A 31 N ILE A 32 1555 1555 1.34 LINK C LYS A 151 N MSE A 152 1555 1555 1.35 LINK C MSE A 152 N VAL A 153 1555 1555 1.31 LINK C ARG A 186 N MSE A 187 1555 1555 1.32 LINK C MSE A 187 N ILE A 188 1555 1555 1.31 LINK C GLY A 218 N MSE A 219 1555 1555 1.34 LINK C MSE A 219 N ALA A 220 1555 1555 1.33 LINK C ALYS A 270 N MSE A 271 1555 1555 1.36 LINK C BLYS A 270 N MSE A 271 1555 1555 1.27 LINK C MSE A 271 N PRO A 272 1555 1555 1.34 LINK C THR A 274 N MSE A 275 1555 1555 1.31 LINK C MSE A 275 N PRO A 276 1555 1555 1.35 LINK C LEU A 278 N MSE A 279 1555 1555 1.34 LINK C MSE A 279 N LEU A 280 1555 1555 1.32 LINK C GLY A 303 N MSE A 304 1555 1555 1.32 LINK C MSE A 304 N TYR A 305 1555 1555 1.33 LINK C GLN A 322 N MSE A 323 1555 1555 1.33 LINK C MSE A 323 N MSE A 324 1555 1555 1.32 LINK C MSE A 324 N GLN A 325 1555 1555 1.32 LINK C ALA A 350 N MSE A 351 1555 1555 1.33 LINK C MSE A 351 N LEU A 352 1555 1555 1.32 CISPEP 1 SER A 40 PRO A 41 0 -4.53 CISPEP 2 MSE A 271 PRO A 272 0 -2.62 SITE 1 AC1 37 GLY A 10 GLY A 12 PRO A 13 GLY A 14 SITE 2 AC1 37 GLU A 33 LYS A 34 ARG A 35 ARG A 43 SITE 3 AC1 37 CYS A 44 GLY A 45 GLU A 46 GLY A 47 SITE 4 AC1 37 ARG A 100 PRO A 123 ALA A 124 ALA A 156 SITE 5 AC1 37 ASP A 157 GLY A 158 GLU A 162 PHE A 213 SITE 6 AC1 37 GLY A 282 ASP A 283 GLY A 294 GLY A 295 SITE 7 AC1 37 ILE A 296 ALA A 299 HOH A 460 HOH A 485 SITE 8 AC1 37 HOH A 489 HOH A 491 HOH A 497 HOH A 499 SITE 9 AC1 37 HOH A 528 HOH A 712 HOH A 715 HOH A 719 SITE 10 AC1 37 HOH A 721 SITE 1 AC2 14 SER A 49 ALA A 207 GLY A 208 TYR A 209 SITE 2 AC2 14 TRP A 211 PRO A 290 ILE A 291 THR A 292 SITE 3 AC2 14 LYS A 338 ALA A 350 SER A 373 HOH A 505 SITE 4 AC2 14 HOH A 569 HOH A 725 SITE 1 AC3 6 ARG A 20 LYS A 24 LEU A 110 LYS A 113 SITE 2 AC3 6 ALA A 114 HOH A 567 SITE 1 AC4 4 TRP A 119 HIS A 141 HOH A 514 HOH A 627 SITE 1 AC5 4 LYS A 138 GLU A 312 GLU A 315 HOH A 473 SITE 1 AC6 4 LYS A 129 GLY A 132 LYS A 133 HOH A 455 SITE 1 AC7 8 LYS A 34 PRO A 123 ALA A 124 LEU A 125 SITE 2 AC7 8 GLU A 162 HOH A 427 HOH A 628 HOH A 670 SITE 1 AC8 2 TYR A 4 HOH A 512 SITE 1 AC9 7 ASN A 177 SER A 227 TRP A 230 LYS A 346 SITE 2 AC9 7 GLU A 347 HOH A 481 HOH A 667 SITE 1 BC1 4 ASP A 289 THR A 292 GLY A 294 ASN A 298 SITE 1 BC2 5 ALA A 297 ASN A 298 ARG A 334 LYS A 338 SITE 2 BC2 5 HOH A 529 SITE 1 BC3 6 ALA A 112 GLY A 115 ALA A 116 ASP A 117 SITE 2 BC3 6 HOH A 484 HOH A 598 SITE 1 BC4 4 TYR A 4 ASP A 117 TRP A 119 HOH A 484 SITE 1 BC5 2 HOH A 450 HOH A 657 SITE 1 BC6 6 ALA A 23 LEU A 27 ALA A 114 HOH A 456 SITE 2 BC6 6 HOH A 556 HOH A 574 SITE 1 BC7 3 THR A 3 LYS A 170 HOH A 458 SITE 1 BC8 2 TYR A 96 THR A 197 CRYST1 49.545 70.622 117.748 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 0.020184 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014160 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008493 0.00000