HEADER TRANSFERASE/TRANSCRIPTION 13-OCT-10 3P8B TITLE X-RAY CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS TRANSCRIPTION TITLE 2 ELONGATION FACTOR SPT4/5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED RNA POLYMERASE, SUBUNIT E''; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TRANSCRIPTION ANTITERMINATION PROTEIN NUSG; COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 GENE: PF0255, SPT4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODONPLUS RIPL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 12 ORGANISM_TAXID: 2261; SOURCE 13 GENE: PF1990, SPT5; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODONPLUS RIPL; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS TRANSCRIPTION ELONGATION FACTOR, RNA POLYMERASE, TRANSFERASE- KEYWDS 2 TRANSCRIPTION COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.S.MURAKAMI,B.J.KLEIN REVDAT 3 21-FEB-24 3P8B 1 REMARK SEQADV LINK REVDAT 2 11-MAY-11 3P8B 1 JRNL REVDAT 1 26-JAN-11 3P8B 0 JRNL AUTH B.J.KLEIN,D.BOSE,K.J.BAKER,Z.M.YUSOFF,X.ZHANG,K.S.MURAKAMI JRNL TITL RNA POLYMERASE AND TRANSCRIPTION ELONGATION FACTOR SPT4/5 JRNL TITL 2 COMPLEX STRUCTURE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 546 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21187417 JRNL DOI 10.1073/PNAS.1013828108 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 41656 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) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2208 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2684 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.3960 REMARK 3 BIN FREE R VALUE SET COUNT : 142 REMARK 3 BIN FREE R VALUE : 0.4070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3238 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.46000 REMARK 3 B22 (A**2) : 1.09000 REMARK 3 B33 (A**2) : -1.55000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.132 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.424 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3343 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4499 ; 1.991 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 410 ; 6.246 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;31.936 ;23.433 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 598 ;18.641 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;20.640 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 512 ; 0.140 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2434 ; 0.010 ; 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): 2062 ; 1.311 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3360 ; 2.244 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1281 ; 3.600 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1139 ; 5.983 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3P8B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000062082. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9181 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44007 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS (PH 5.5), 0.2 M NACL, REMARK 280 AND 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.60650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.55350 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.60650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 66.55350 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 MET B 1 REMARK 465 GLN B 149 REMARK 465 LYS B 150 REMARK 465 GLU B 151 REMARK 465 GLU B 152 REMARK 465 MET C -19 REMARK 465 GLY C -18 REMARK 465 SER C -17 REMARK 465 SER C -16 REMARK 465 HIS C -15 REMARK 465 HIS C -14 REMARK 465 HIS C -13 REMARK 465 HIS C -12 REMARK 465 HIS C -11 REMARK 465 HIS C -10 REMARK 465 SER C -9 REMARK 465 SER C -8 REMARK 465 GLY C -7 REMARK 465 LEU C -6 REMARK 465 VAL C -5 REMARK 465 PRO C -4 REMARK 465 ARG C -3 REMARK 465 GLY C -2 REMARK 465 SER C -1 REMARK 465 HIS C 0 REMARK 465 MET C 1 REMARK 465 MET D 1 REMARK 465 GLN D 149 REMARK 465 LYS D 150 REMARK 465 GLU D 151 REMARK 465 GLU D 152 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 O1 BME D 155 O HOH D 190 1.94 REMARK 500 CG GLU B 84 O HOH B 172 2.12 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 59 NE - CZ - NH1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG A 59 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG C 59 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG C 59 NE - CZ - NH2 ANGL. DEV. = -4.8 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 ASP A 32 94.21 65.65 REMARK 500 HIS C 10 -2.43 89.11 REMARK 500 ASP C 32 92.43 72.10 REMARK 500 HIS D 65 -16.92 92.15 REMARK 500 HIS D 81 3.14 -68.42 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 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 CYS A 9 SG 111.3 REMARK 620 3 CYS A 18 SG 110.4 103.3 REMARK 620 4 CYS A 21 SG 98.8 117.3 116.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 6 SG REMARK 620 2 CYS C 9 SG 117.1 REMARK 620 3 CYS C 18 SG 107.2 108.0 REMARK 620 4 CYS C 21 SG 97.3 116.6 110.1 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 62 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 153 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 154 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME B 156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME B 157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME B 158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 153 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 154 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME D 155 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME D 156 DBREF 3P8B A 1 61 UNP Q8U440 Q8U440_PYRFU 1 61 DBREF 3P8B B 1 152 UNP Q8TZK1 Q8TZK1_PYRFU 1 152 DBREF 3P8B C 1 61 UNP Q8U440 Q8U440_PYRFU 1 61 DBREF 3P8B D 1 152 UNP Q8TZK1 Q8TZK1_PYRFU 1 152 SEQADV 3P8B MET A -19 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B GLY A -18 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B SER A -17 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B SER A -16 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS A -15 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS A -14 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS A -13 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS A -12 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS A -11 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS A -10 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B SER A -9 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B SER A -8 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B GLY A -7 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B LEU A -6 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B VAL A -5 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B PRO A -4 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B ARG A -3 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B GLY A -2 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B SER A -1 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS A 0 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B MET C -19 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B GLY C -18 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B SER C -17 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B SER C -16 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS C -15 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS C -14 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS C -13 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS C -12 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS C -11 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS C -10 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B SER C -9 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B SER C -8 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B GLY C -7 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B LEU C -6 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B VAL C -5 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B PRO C -4 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B ARG C -3 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B GLY C -2 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B SER C -1 UNP Q8U440 EXPRESSION TAG SEQADV 3P8B HIS C 0 UNP Q8U440 EXPRESSION TAG SEQRES 1 A 81 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 81 LEU VAL PRO ARG GLY SER HIS MET SER GLU LYS ALA CYS SEQRES 3 A 81 ARG HIS CYS HIS TYR ILE THR SER GLU ASP ARG CYS PRO SEQRES 4 A 81 VAL CYS GLY SER ARG ASP LEU SER GLU GLU TRP PHE ASP SEQRES 5 A 81 LEU VAL ILE ILE VAL ASP VAL GLU ASN SER GLU ILE ALA SEQRES 6 A 81 LYS LYS ILE GLY ALA LYS VAL PRO GLY LYS TYR ALA ILE SEQRES 7 A 81 ARG VAL ARG SEQRES 1 B 152 MET ALA GLY LYS ILE PHE ALA VAL ARG VAL THR HIS GLY SEQRES 2 B 152 GLN GLU GLU THR THR ALA LYS LEU ILE TYR SER LYS VAL SEQRES 3 B 152 ARG THR TYR ASN LEU PRO ILE TYR ALA ILE LEU ALA PRO SEQRES 4 B 152 SER ARG VAL LYS GLY TYR ILE PHE VAL GLU ALA PRO ASN SEQRES 5 B 152 LYS GLY VAL VAL ASP GLU ALA ILE ARG GLY ILE ARG HIS SEQRES 6 B 152 ALA ARG GLY VAL LEU PRO GLY GLU VAL PRO PHE LYS GLU SEQRES 7 B 152 ILE GLU HIS PHE LEU GLU GLU LYS PRO ALA VAL SER GLY SEQRES 8 B 152 LEU GLU PRO GLY ASP LEU VAL GLU VAL ILE ALA GLY PRO SEQRES 9 B 152 PHE LYS GLY GLN LYS ALA LYS VAL VAL LYS ILE ASP GLU SEQRES 10 B 152 SER LYS ASP GLU VAL VAL VAL GLN PHE ILE ASP ALA ILE SEQRES 11 B 152 VAL PRO ILE PRO VAL THR ILE LYS GLY ASP TYR VAL ARG SEQRES 12 B 152 LEU ILE SER LYS LEU GLN LYS GLU GLU SEQRES 1 C 81 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 C 81 LEU VAL PRO ARG GLY SER HIS MET SER GLU LYS ALA CYS SEQRES 3 C 81 ARG HIS CYS HIS TYR ILE THR SER GLU ASP ARG CYS PRO SEQRES 4 C 81 VAL CYS GLY SER ARG ASP LEU SER GLU GLU TRP PHE ASP SEQRES 5 C 81 LEU VAL ILE ILE VAL ASP VAL GLU ASN SER GLU ILE ALA SEQRES 6 C 81 LYS LYS ILE GLY ALA LYS VAL PRO GLY LYS TYR ALA ILE SEQRES 7 C 81 ARG VAL ARG SEQRES 1 D 152 MET ALA GLY LYS ILE PHE ALA VAL ARG VAL THR HIS GLY SEQRES 2 D 152 GLN GLU GLU THR THR ALA LYS LEU ILE TYR SER LYS VAL SEQRES 3 D 152 ARG THR TYR ASN LEU PRO ILE TYR ALA ILE LEU ALA PRO SEQRES 4 D 152 SER ARG VAL LYS GLY TYR ILE PHE VAL GLU ALA PRO ASN SEQRES 5 D 152 LYS GLY VAL VAL ASP GLU ALA ILE ARG GLY ILE ARG HIS SEQRES 6 D 152 ALA ARG GLY VAL LEU PRO GLY GLU VAL PRO PHE LYS GLU SEQRES 7 D 152 ILE GLU HIS PHE LEU GLU GLU LYS PRO ALA VAL SER GLY SEQRES 8 D 152 LEU GLU PRO GLY ASP LEU VAL GLU VAL ILE ALA GLY PRO SEQRES 9 D 152 PHE LYS GLY GLN LYS ALA LYS VAL VAL LYS ILE ASP GLU SEQRES 10 D 152 SER LYS ASP GLU VAL VAL VAL GLN PHE ILE ASP ALA ILE SEQRES 11 D 152 VAL PRO ILE PRO VAL THR ILE LYS GLY ASP TYR VAL ARG SEQRES 12 D 152 LEU ILE SER LYS LEU GLN LYS GLU GLU HET ZN A 101 1 HET BME A 62 4 HET GOL B 153 6 HET GOL B 154 6 HET GOL B 155 6 HET BME B 156 4 HET BME B 157 4 HET BME B 158 4 HET ZN C 101 1 HET GOL D 153 6 HET GOL D 154 6 HET BME D 155 4 HET BME D 156 4 HETNAM ZN ZINC ION HETNAM BME BETA-MERCAPTOETHANOL HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 ZN 2(ZN 2+) FORMUL 6 BME 6(C2 H6 O S) FORMUL 7 GOL 5(C3 H8 O3) FORMUL 18 HOH *111(H2 O) HELIX 1 1 SER A 42 GLY A 49 1 8 HELIX 2 2 GLN B 14 ASN B 30 1 17 HELIX 3 3 ASN B 52 ARG B 61 1 10 HELIX 4 4 PRO B 75 LEU B 83 5 9 HELIX 5 5 SER C 42 GLY C 49 1 8 HELIX 6 6 GLN D 14 TYR D 29 1 16 HELIX 7 7 ASN D 52 ILE D 60 1 9 HELIX 8 8 PRO D 75 LEU D 83 5 9 HELIX 9 9 ALA D 102 LYS D 106 5 5 SHEET 1 A 3 ILE A 12 THR A 13 0 SHEET 2 A 3 LYS A 4 CYS A 6 -1 N LYS A 4 O THR A 13 SHEET 3 A 3 LEU A 26 SER A 27 -1 O SER A 27 N ALA A 5 SHEET 1 B 6 GLY A 54 VAL A 60 0 SHEET 2 B 6 TRP A 30 ILE A 36 -1 N VAL A 34 O TYR A 56 SHEET 3 B 6 ALA B 35 ALA B 38 -1 O ILE B 36 N ILE A 35 SHEET 4 B 6 TYR B 45 ALA B 50 -1 O GLU B 49 N ALA B 35 SHEET 5 B 6 LYS B 4 VAL B 10 -1 N LYS B 4 O ALA B 50 SHEET 6 B 6 ALA B 66 VAL B 69 -1 O ARG B 67 N ARG B 9 SHEET 1 C 5 PRO B 134 LYS B 138 0 SHEET 2 C 5 GLU B 121 PHE B 126 -1 N VAL B 124 O VAL B 135 SHEET 3 C 5 LYS B 109 ASP B 116 -1 N LYS B 114 O VAL B 123 SHEET 4 C 5 LEU B 97 VAL B 100 -1 N VAL B 98 O ALA B 110 SHEET 5 C 5 VAL B 142 SER B 146 -1 O SER B 146 N LEU B 97 SHEET 1 D 3 ILE C 12 THR C 13 0 SHEET 2 D 3 LYS C 4 CYS C 6 -1 N LYS C 4 O THR C 13 SHEET 3 D 3 LEU C 26 SER C 27 -1 O SER C 27 N ALA C 5 SHEET 1 E 6 GLY C 54 VAL C 60 0 SHEET 2 E 6 TRP C 30 ILE C 36 -1 N ILE C 36 O GLY C 54 SHEET 3 E 6 ALA D 35 ALA D 38 -1 O ILE D 36 N ILE C 35 SHEET 4 E 6 TYR D 45 ALA D 50 -1 O GLU D 49 N ALA D 35 SHEET 5 E 6 LYS D 4 VAL D 10 -1 N LYS D 4 O ALA D 50 SHEET 6 E 6 ALA D 66 VAL D 69 -1 O ARG D 67 N ARG D 9 SHEET 1 F 5 VAL D 135 LYS D 138 0 SHEET 2 F 5 GLU D 121 PHE D 126 -1 N VAL D 124 O VAL D 135 SHEET 3 F 5 LYS D 109 ASP D 116 -1 N VAL D 113 O VAL D 123 SHEET 4 F 5 LEU D 97 VAL D 100 -1 N VAL D 98 O ALA D 110 SHEET 5 F 5 VAL D 142 SER D 146 -1 O SER D 146 N LEU D 97 LINK SG CYS A 6 ZN ZN A 101 1555 1555 2.27 LINK SG CYS A 9 ZN ZN A 101 1555 1555 2.45 LINK SG CYS A 18 ZN ZN A 101 1555 1555 2.24 LINK SG CYS A 21 ZN ZN A 101 1555 1555 2.29 LINK SG CYS C 6 ZN ZN C 101 1555 1555 2.27 LINK SG CYS C 9 ZN ZN C 101 1555 1555 2.40 LINK SG CYS C 18 ZN ZN C 101 1555 1555 2.41 LINK SG CYS C 21 ZN ZN C 101 1555 1555 2.43 SITE 1 AC1 4 CYS A 6 CYS A 9 CYS A 18 CYS A 21 SITE 1 AC2 1 GLU A 3 SITE 1 AC3 4 GLU A 3 TRP A 30 GLU B 16 SER B 40 SITE 1 AC4 8 ARG A 61 HOH A 92 GLU B 84 LYS B 86 SITE 2 AC4 8 ASP B 120 ASP B 140 HOH B 164 PRO D 104 SITE 1 AC5 7 GLY B 62 HOH B 185 VAL C 37 ASP C 38 SITE 2 AC5 7 ASN D 30 LEU D 31 ILE D 33 SITE 1 AC6 7 VAL A 37 ASP A 38 VAL B 26 ASN B 30 SITE 2 AC6 7 LEU B 31 ILE B 33 ARG D 61 SITE 1 AC7 4 GLN B 108 LYS B 109 ILE B 127 ASP B 128 SITE 1 AC8 6 PHE B 105 PHE B 126 ALA B 129 VAL B 131 SITE 2 AC8 6 HOH B 171 GLU D 78 SITE 1 AC9 4 CYS C 6 CYS C 9 CYS C 18 CYS C 21 SITE 1 BC1 3 TRP C 30 GLU D 16 SER D 40 SITE 1 BC2 6 ARG D 9 VAL D 10 HIS D 12 GLY D 44 SITE 2 BC2 6 TYR D 45 HOH D 164 SITE 1 BC3 6 GLU B 78 PHE D 126 ALA D 129 VAL D 131 SITE 2 BC3 6 ILE D 133 HOH D 190 SITE 1 BC4 5 THR B 136 ILE B 137 LYS B 138 TYR B 141 SITE 2 BC4 5 ARG D 41 CRYST1 40.532 87.213 133.107 90.00 90.00 90.00 P 2 21 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 0.024672 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011466 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007513 0.00000