HEADER NUCLEAR PROTEIN 13-OCT-04 1W9H TITLE THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN AF1318; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PIWI; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARCHAEOGLOBUS FULGIDUS; SOURCE 3 ORGANISM_TAXID: 2234; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET-17B KEYWDS ARGONAUTE, PIWI DOMAIN, RNAI, RISC, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.S.PARKER,S.M.ROE,D.BARFORD REVDAT 3 05-JUL-17 1W9H 1 REMARK REVDAT 2 24-FEB-09 1W9H 1 VERSN REVDAT 1 13-JAN-05 1W9H 0 JRNL AUTH J.S.PARKER,S.M.ROE,D.BARFORD JRNL TITL CRYSTAL STRUCTURE OF A PIWI PROTEIN SUGGESTS MECHANISMS FOR JRNL TITL 2 SIRNA RECOGNITION AND SLICER ACTIVITY JRNL REF EMBO J. V. 23 4727 2004 JRNL REFN ISSN 0261-4189 JRNL PMID 15565169 JRNL DOI 10.1038/SJ.EMBOJ.7600488 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 34383 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1814 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2155 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3233 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.95000 REMARK 3 B22 (A**2) : 1.83000 REMARK 3 B33 (A**2) : -0.88000 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): 0.158 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.539 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3313 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4499 ; 1.635 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 394 ; 6.303 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 146 ;40.712 ;24.589 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 585 ;14.933 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;12.412 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 501 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2469 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1602 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2279 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 239 ; 0.207 ; 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): 53 ; 0.273 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.200 ; 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): 2068 ; 1.188 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3250 ; 1.800 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1477 ; 2.852 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1249 ; 4.047 ; 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 : 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 11 A 171 REMARK 3 ORIGIN FOR THE GROUP (A): 35.0372 19.9316 32.4247 REMARK 3 T TENSOR REMARK 3 T11: -0.1347 T22: -0.1204 REMARK 3 T33: -0.1125 T12: -0.0071 REMARK 3 T13: 0.0158 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 4.8760 L22: 1.0808 REMARK 3 L33: 4.1255 L12: 1.3188 REMARK 3 L13: 2.7216 L23: 0.7599 REMARK 3 S TENSOR REMARK 3 S11: 0.1653 S12: -0.0069 S13: -0.4927 REMARK 3 S21: -0.0157 S22: 0.0442 S23: -0.3273 REMARK 3 S31: 0.4523 S32: 0.3809 S33: -0.2094 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 172 A 427 REMARK 3 ORIGIN FOR THE GROUP (A): 9.9090 20.5201 42.8313 REMARK 3 T TENSOR REMARK 3 T11: -0.1672 T22: -0.1778 REMARK 3 T33: -0.1922 T12: -0.0458 REMARK 3 T13: -0.0244 T23: 0.0264 REMARK 3 L TENSOR REMARK 3 L11: 2.3867 L22: 1.8049 REMARK 3 L33: 2.4629 L12: 0.1019 REMARK 3 L13: -0.1197 L23: -0.1225 REMARK 3 S TENSOR REMARK 3 S11: -0.0002 S12: -0.0603 S13: -0.0660 REMARK 3 S21: 0.0965 S22: -0.0749 S23: 0.0707 REMARK 3 S31: -0.1063 S32: -0.0474 S33: 0.0751 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 1W9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1290021312. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.931 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 143262 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.16000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SNB, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION AT 10 MG/ML WAS MIXED REMARK 280 WITH A SOLUTION CONTAINING 0.1 M SODIUM ACETATE PH 4.6, 0.1 M REMARK 280 CADMIUM CHLORIDE, 30% PEG 400, 5 MM DTT. CRYSTALS COULD BE REMARK 280 OBTAINED REPRODUCIBLY BY STREAK SEEDING IN TO THE REMARK 280 CRYSTALLISATION SOLUTION AFTER A 3 HOUR EQUILIBRATION. CRYSTALS REMARK 280 APPEARED AFTER 2-3 DAYS AND GREW AFTER 5 DAYS TO A FINAL SIZE OF REMARK 280 0.1 MM X 0.1 MM X 0.1 MM, PH 4.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,Y+1/2,-Z 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 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 34.54500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 68.93150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.54500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 68.93150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 MET A 1 REMARK 465 MET A 2 REMARK 465 GLU A 3 REMARK 465 TYR A 4 REMARK 465 LYS A 5 REMARK 465 ILE A 6 REMARK 465 VAL A 7 REMARK 465 GLU A 8 REMARK 465 ASN A 9 REMARK 465 GLY A 10 REMARK 465 LEU A 144 REMARK 465 SER A 145 REMARK 465 ASN A 146 REMARK 465 ARG A 147 REMARK 465 ASN A 148 REMARK 465 GLY A 302 REMARK 465 ASP A 303 REMARK 465 PRO A 304 REMARK 465 ASN A 305 REMARK 465 ASN A 306 REMARK 465 ARG A 307 REMARK 465 PHE A 308 REMARK 465 LYS A 333 REMARK 465 ARG A 334 REMARK 465 ASN A 335 REMARK 465 GLY A 336 REMARK 465 LEU A 337 REMARK 465 GLU A 338 REMARK 465 MET A 339 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 HIS A 309 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 332 CG CD1 CD2 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 ND2 ASN A 378 O HOH A 2208 2.03 REMARK 500 CE1 HIS A 362 OE2 GLU A 366 2.03 REMARK 500 OD1 ASP A 154 O HOH A 2089 2.06 REMARK 500 O HOH A 2094 O HOH A 2095 2.15 REMARK 500 O HOH A 2018 O HOH A 2039 2.17 REMARK 500 OH TYR A 123 O HOH A 2075 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 55 C GLN A 56 N -0.159 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 LEU A 130 CA - CB - CG ANGL. DEV. = -17.0 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 ILE A 15 -148.90 -114.23 REMARK 500 PHE A 57 75.81 49.79 REMARK 500 TYR A 118 50.93 -114.54 REMARK 500 ILE A 134 145.49 -172.02 REMARK 500 LYS A 259 86.83 -68.21 REMARK 500 LYS A 261 -77.56 -60.46 REMARK 500 GLN A 278 13.78 -69.83 REMARK 500 TYR A 311 73.49 -106.39 REMARK 500 GLU A 312 -78.36 -146.41 REMARK 500 ASN A 378 110.99 -160.39 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 CD A1428 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 427 OXT REMARK 620 2 CL A1435 CL 102.6 REMARK 620 3 GLN A 159 OE1 81.8 88.8 REMARK 620 4 LEU A 427 O 52.1 154.6 86.4 REMARK 620 5 CL A1436 CL 145.7 111.4 93.6 93.8 REMARK 620 6 HOH A2080 O 93.3 93.4 175.0 89.8 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1429 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 99 OE1 REMARK 620 2 CL A1438 CL 103.3 REMARK 620 3 SER A 357 OG 80.6 172.5 REMARK 620 4 GLU A 358 OE1 141.1 93.9 79.3 REMARK 620 5 GLU A 358 OE2 87.4 102.3 71.2 54.7 REMARK 620 6 CL A1437 CL 107.7 98.3 86.5 103.9 150.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1430 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2037 O REMARK 620 2 HOH A2146 O 173.5 REMARK 620 3 ASP A 73 OD1 88.6 86.9 REMARK 620 4 ASP A 73 OD2 71.4 109.0 50.1 REMARK 620 5 ASP A 245 OD1 77.4 101.4 124.4 148.2 REMARK 620 6 ASP A 245 OD2 80.7 93.4 71.5 114.2 53.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1431 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2043 O REMARK 620 2 ASP A 284 OD1 149.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1432 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 291 ND1 REMARK 620 2 HOH A2168 O 90.5 REMARK 620 3 HOH A2189 O 106.7 108.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1433 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2177 O REMARK 620 2 ASP A 369 OD2 128.4 REMARK 620 3 HOH A2205 O 141.8 87.2 REMARK 620 4 HIS A 365 NE2 108.7 76.3 91.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1434 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2140 O REMARK 620 2 ASP A 105 OD2 125.7 REMARK 620 3 HOH A2056 O 89.3 107.3 REMARK 620 4 ASP A 105 OD1 109.1 51.1 157.2 REMARK 620 N 1 2 3 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A1428 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A1429 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A1430 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A1431 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A1432 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A1433 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A1434 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1435 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1436 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1437 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1438 DBREF 1W9H A 1 427 UNP O28951 O28951 1 427 SEQRES 1 A 427 MET MET GLU TYR LYS ILE VAL GLU ASN GLY LEU THR TYR SEQRES 2 A 427 ARG ILE GLY ASN GLY ALA SER VAL PRO ILE SER ASN THR SEQRES 3 A 427 GLY GLU LEU ILE LYS GLY LEU ARG ASN TYR GLY PRO TYR SEQRES 4 A 427 GLU VAL PRO SER LEU LYS TYR ASN GLN ILE ALA LEU ILE SEQRES 5 A 427 HIS ASN ASN GLN PHE SER SER LEU ILE ASN GLN LEU LYS SEQRES 6 A 427 SER GLN ILE SER SER LYS ILE ASP GLU VAL TRP HIS ILE SEQRES 7 A 427 HIS ASN ILE ASN ILE SER GLU PHE ILE TYR ASP SER PRO SEQRES 8 A 427 HIS PHE ASP SER ILE LYS SER GLN VAL ASP ASN ALA ILE SEQRES 9 A 427 ASP THR GLY VAL ASP GLY ILE MET LEU VAL LEU PRO GLU SEQRES 10 A 427 TYR ASN THR PRO LEU TYR TYR LYS LEU LYS SER TYR LEU SEQRES 11 A 427 ILE ASN SER ILE PRO SER GLN PHE MET ARG TYR ASP ILE SEQRES 12 A 427 LEU SER ASN ARG ASN LEU THR PHE TYR VAL ASP ASN LEU SEQRES 13 A 427 LEU VAL GLN PHE VAL SER LYS LEU GLY GLY LYS PRO TRP SEQRES 14 A 427 ILE LEU ASN VAL ASP PRO GLU LYS GLY SER ASP ILE ILE SEQRES 15 A 427 ILE GLY THR GLY ALA THR ARG ILE ASP ASN VAL ASN LEU SEQRES 16 A 427 PHE CYS PHE ALA MET VAL PHE LYS LYS ASP GLY THR MET SEQRES 17 A 427 LEU TRP ASN GLU ILE SER PRO ILE VAL THR SER SER GLU SEQRES 18 A 427 TYR LEU THR TYR LEU LYS SER THR ILE LYS LYS VAL VAL SEQRES 19 A 427 TYR GLY PHE LYS LYS SER ASN PRO ASP TRP ASP VAL GLU SEQRES 20 A 427 LYS LEU THR LEU HIS VAL SER GLY LYS ARG PRO LYS MET SEQRES 21 A 427 LYS ASP GLY GLU THR LYS ILE LEU LYS GLU THR VAL GLU SEQRES 22 A 427 GLU LEU LYS LYS GLN GLU MET VAL SER ARG ASP VAL LYS SEQRES 23 A 427 TYR ALA ILE LEU HIS LEU ASN GLU THR HIS PRO PHE TRP SEQRES 24 A 427 VAL MET GLY ASP PRO ASN ASN ARG PHE HIS PRO TYR GLU SEQRES 25 A 427 GLY THR LYS VAL LYS LEU SER SER LYS ARG TYR LEU LEU SEQRES 26 A 427 THR LEU LEU GLN PRO TYR LEU LYS ARG ASN GLY LEU GLU SEQRES 27 A 427 MET VAL THR PRO ILE LYS PRO LEU SER VAL GLU ILE VAL SEQRES 28 A 427 SER ASP ASN TRP THR SER GLU GLU TYR TYR HIS ASN VAL SEQRES 29 A 427 HIS GLU ILE LEU ASP GLU ILE TYR TYR LEU SER LYS MET SEQRES 30 A 427 ASN TRP ARG GLY PHE ARG SER ARG ASN LEU PRO VAL THR SEQRES 31 A 427 VAL ASN TYR PRO LYS LEU VAL ALA GLY ILE ILE ALA ASN SEQRES 32 A 427 VAL ASN ARG TYR GLY GLY TYR PRO ILE ASN PRO GLU GLY SEQRES 33 A 427 ASN ARG SER LEU GLN THR ASN PRO TRP PHE LEU HET CD A1428 1 HET CD A1429 1 HET NI A1430 1 HET NI A1431 1 HET NI A1432 1 HET NI A1433 1 HET NI A1434 1 HET CL A1435 1 HET CL A1436 1 HET CL A1437 1 HET CL A1438 1 HETNAM CD CADMIUM ION HETNAM NI NICKEL (II) ION HETNAM CL CHLORIDE ION FORMUL 2 CD 2(CD 2+) FORMUL 4 NI 5(NI 2+) FORMUL 9 CL 4(CL 1-) FORMUL 13 HOH *238(H2 O) HELIX 1 1 GLY A 16 GLY A 18 5 3 HELIX 2 2 ASN A 25 GLY A 37 1 13 HELIX 3 3 PHE A 57 VAL A 75 1 19 HELIX 4 4 HIS A 92 GLY A 107 1 16 HELIX 5 5 ASN A 119 ASN A 132 1 14 HELIX 6 6 LEU A 149 LEU A 164 1 16 HELIX 7 7 ASP A 174 GLY A 178 5 5 HELIX 8 8 GLU A 221 ASN A 241 1 21 HELIX 9 9 MET A 260 GLN A 278 1 19 HELIX 10 10 GLU A 359 SER A 375 1 17 HELIX 11 11 PRO A 388 GLY A 408 1 21 HELIX 12 12 ASN A 417 ASN A 423 1 7 SHEET 1 AA 3 SER A 20 PRO A 22 0 SHEET 2 AA 3 THR A 12 ARG A 14 -1 O TYR A 13 N VAL A 21 SHEET 3 AA 3 ILE A 170 LEU A 171 -1 O ILE A 170 N ARG A 14 SHEET 1 AB 4 ASN A 82 ILE A 87 0 SHEET 2 AB 4 GLN A 48 HIS A 53 1 O ILE A 49 N SER A 84 SHEET 3 AB 4 GLY A 110 LEU A 115 1 O GLY A 110 N ALA A 50 SHEET 4 AB 4 SER A 136 ARG A 140 1 O GLN A 137 N LEU A 113 SHEET 1 AC 8 MET A 208 ILE A 213 0 SHEET 2 AC 8 ASN A 194 LYS A 203 -1 O ALA A 199 N GLU A 212 SHEET 3 AC 8 ILE A 181 ARG A 189 -1 O ILE A 182 N PHE A 202 SHEET 4 AC 8 LYS A 248 SER A 254 1 O LYS A 248 N ILE A 181 SHEET 5 AC 8 LYS A 286 GLU A 294 1 O LYS A 286 N LEU A 249 SHEET 6 AC 8 LEU A 346 ASP A 353 -1 O SER A 347 N ASN A 293 SHEET 7 AC 8 ARG A 322 LEU A 325 -1 O TYR A 323 N VAL A 348 SHEET 8 AC 8 LYS A 315 LYS A 317 -1 O VAL A 316 N LEU A 324 SHEET 1 AD 3 MET A 208 ILE A 213 0 SHEET 2 AD 3 ASN A 194 LYS A 203 -1 O ALA A 199 N GLU A 212 SHEET 3 AD 3 VAL A 217 THR A 218 -1 O VAL A 217 N LEU A 195 SHEET 1 AE 2 PHE A 298 VAL A 300 0 SHEET 2 AE 2 THR A 341 ILE A 343 -1 O THR A 341 N VAL A 300 LINK CD CD A1428 OXT LEU A 427 1555 1555 2.39 LINK CD CD A1428 CL CL A1435 1555 1555 2.57 LINK CD CD A1428 OE1 GLN A 159 1555 1555 2.45 LINK CD CD A1428 O LEU A 427 1555 1555 2.59 LINK CD CD A1428 CL CL A1436 1555 1555 2.69 LINK CD CD A1428 O HOH A2080 1555 1555 2.53 LINK CD CD A1429 OE1 GLN A 99 1555 1555 2.42 LINK CD CD A1429 CL CL A1438 1555 1555 2.31 LINK CD CD A1429 OG SER A 357 1555 1655 2.94 LINK CD CD A1429 OE1 GLU A 358 1555 1655 2.47 LINK CD CD A1429 OE2 GLU A 358 1555 1655 2.23 LINK CD CD A1429 CL CL A1437 1555 1555 2.43 LINK NI NI A1430 O HOH A2037 1555 1555 1.47 LINK NI NI A1430 O HOH A2146 1555 4556 2.36 LINK NI NI A1430 OD1 ASP A 73 1555 1555 2.76 LINK NI NI A1430 OD2 ASP A 73 1555 1555 2.33 LINK NI NI A1430 OD1 ASP A 245 1555 4556 2.48 LINK NI NI A1430 OD2 ASP A 245 1555 4556 2.43 LINK NI NI A1431 O HOH A2043 1555 4456 2.72 LINK NI NI A1431 OD1 ASP A 284 1555 1555 2.40 LINK NI NI A1432 ND1 HIS A 291 1555 1555 2.42 LINK NI NI A1432 O HOH A2168 1555 1555 1.95 LINK NI NI A1432 O HOH A2189 1555 1555 2.51 LINK NI NI A1433 O HOH A2177 1555 1555 2.42 LINK NI NI A1433 OD2 ASP A 369 1555 1555 2.41 LINK NI NI A1433 O HOH A2205 1555 1555 2.67 LINK NI NI A1433 NE2 HIS A 365 1555 1555 2.24 LINK NI NI A1434 O HOH A2140 1555 4557 2.08 LINK NI NI A1434 OD2 ASP A 105 1555 1555 2.56 LINK NI NI A1434 O HOH A2056 1555 4557 2.58 LINK NI NI A1434 OD1 ASP A 105 1555 1555 2.52 SITE 1 AC1 5 GLN A 159 LEU A 427 CL A1435 CL A1436 SITE 2 AC1 5 HOH A2080 SITE 1 AC2 5 GLN A 99 SER A 357 GLU A 358 CL A1437 SITE 2 AC2 5 CL A1438 SITE 1 AC3 4 ASP A 73 ASP A 245 HOH A2037 HOH A2146 SITE 1 AC4 4 HIS A 79 GLU A 247 ASP A 284 HOH A2043 SITE 1 AC5 5 HIS A 291 GLU A 349 HOH A2168 HOH A2189 SITE 2 AC5 5 HOH A2190 SITE 1 AC6 4 HIS A 365 ASP A 369 HOH A2177 HOH A2205 SITE 1 AC7 3 ASP A 105 HOH A2056 HOH A2140 SITE 1 AC8 3 GLN A 159 ARG A 380 CD A1428 SITE 1 AC9 5 LYS A 127 GLN A 137 PHE A 138 LYS A 163 SITE 2 AC9 5 CD A1428 SITE 1 BC1 4 GLN A 99 SER A 357 CD A1429 CL A1438 SITE 1 BC2 5 PHE A 86 ASN A 102 GLU A 358 CD A1429 SITE 2 BC2 5 CL A1437 CRYST1 69.090 137.863 51.663 90.00 90.00 90.00 P 21 21 2 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 0.014474 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007254 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019356 0.00000