HEADER HYDROLASE 24-DEC-15 5H8W TITLE XPD MECHANISM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT DNA HELICASE TA0057; COMPND 3 CHAIN: A; COMPND 4 EC: 3.6.4.12; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(P*TP*AP*CP*GP*A)-3'); COMPND 8 CHAIN: E; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOPLASMA ACIDOPHILUM; SOURCE 3 ORGANISM_TAXID: 2303; SOURCE 4 GENE: TA0057; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 562 KEYWDS HELICASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.H.NAISMITH,D.CONSTANTINESCU REVDAT 4 20-APR-16 5H8W 1 JRNL REVDAT 3 02-MAR-16 5H8W 1 JRNL REVDAT 2 20-JAN-16 5H8W 1 REVDAT 1 13-JAN-16 5H8W 0 JRNL AUTH D.CONSTANTINESCU-ARUXANDEI,B.PETROVIC-STOJANOVSKA, JRNL AUTH 2 J.C.PENEDO,M.F.WHITE,J.H.NAISMITH JRNL TITL MECHANISM OF DNA LOADING BY THE DNA REPAIR HELICASE XPD. JRNL REF NUCLEIC ACIDS RES. V. 44 2806 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 26896802 JRNL DOI 10.1093/NAR/GKW102 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 29691 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1469 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2225 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.57 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE SET COUNT : 98 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4792 REMARK 3 NUCLEIC ACID ATOMS : 87 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : -1.54000 REMARK 3 B12 (A**2) : 0.24000 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): 0.329 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.223 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.185 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.206 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5023 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4754 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6822 ; 1.467 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10964 ; 1.283 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 601 ; 6.069 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 235 ;32.859 ;23.404 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 907 ;15.832 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;21.447 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 723 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5552 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1152 ; 0.001 ; 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): 2389 ; 0.604 ; 2.215 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2388 ; 0.604 ; 2.215 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2986 ; 1.070 ; 3.319 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2987 ; 1.070 ; 3.319 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2634 ; 0.642 ; 2.288 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2630 ; 0.642 ; 2.288 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3769 ; 1.009 ; 3.392 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5494 ; 2.318 ;17.242 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5481 ; 2.295 ;17.202 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 : 6 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 20 A 223 REMARK 3 ORIGIN FOR THE GROUP (A): 57.3530 55.5880 -15.2400 REMARK 3 T TENSOR REMARK 3 T11: 0.1644 T22: 0.0310 REMARK 3 T33: 0.2151 T12: -0.0144 REMARK 3 T13: -0.0702 T23: -0.0329 REMARK 3 L TENSOR REMARK 3 L11: 2.1881 L22: 3.0534 REMARK 3 L33: 1.0149 L12: -1.6696 REMARK 3 L13: 0.1642 L23: -0.4534 REMARK 3 S TENSOR REMARK 3 S11: 0.2282 S12: 0.1905 S13: -0.3823 REMARK 3 S21: -0.3210 S22: -0.1109 S23: 0.2780 REMARK 3 S31: 0.1498 S32: -0.0831 S33: -0.1173 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 224 A 338 REMARK 3 ORIGIN FOR THE GROUP (A): 66.8420 67.1070 16.5120 REMARK 3 T TENSOR REMARK 3 T11: 0.1055 T22: 0.1151 REMARK 3 T33: 0.1866 T12: -0.0760 REMARK 3 T13: 0.0344 T23: -0.0525 REMARK 3 L TENSOR REMARK 3 L11: 4.5186 L22: 2.1281 REMARK 3 L33: 1.8781 L12: -0.9717 REMARK 3 L13: 0.6748 L23: 0.5390 REMARK 3 S TENSOR REMARK 3 S11: 0.0433 S12: -0.4677 S13: 0.2137 REMARK 3 S21: 0.0566 S22: 0.1138 S23: -0.2474 REMARK 3 S31: -0.1213 S32: 0.1860 S33: -0.1571 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 339 A 405 REMARK 3 ORIGIN FOR THE GROUP (A): 74.3440 46.4640 -3.0000 REMARK 3 T TENSOR REMARK 3 T11: 0.1712 T22: 0.0421 REMARK 3 T33: 0.2892 T12: 0.0076 REMARK 3 T13: -0.0148 T23: 0.0130 REMARK 3 L TENSOR REMARK 3 L11: 2.1671 L22: 3.1868 REMARK 3 L33: 2.9344 L12: 0.4380 REMARK 3 L13: 0.4663 L23: 2.2489 REMARK 3 S TENSOR REMARK 3 S11: 0.1833 S12: -0.1836 S13: -0.2357 REMARK 3 S21: 0.0017 S22: 0.0593 S23: -0.1952 REMARK 3 S31: 0.2226 S32: 0.2032 S33: -0.2426 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 406 A 525 REMARK 3 ORIGIN FOR THE GROUP (A): 91.6290 62.6820 -21.2330 REMARK 3 T TENSOR REMARK 3 T11: 0.1377 T22: 0.0592 REMARK 3 T33: 0.1961 T12: 0.0619 REMARK 3 T13: 0.0213 T23: -0.0188 REMARK 3 L TENSOR REMARK 3 L11: 3.0353 L22: 3.0615 REMARK 3 L33: 3.1362 L12: 0.1989 REMARK 3 L13: -0.5252 L23: 0.3112 REMARK 3 S TENSOR REMARK 3 S11: 0.0446 S12: -0.0224 S13: 0.1281 REMARK 3 S21: -0.0598 S22: -0.0585 S23: 0.0212 REMARK 3 S31: -0.1707 S32: -0.2461 S33: 0.0139 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 526 A 615 REMARK 3 ORIGIN FOR THE GROUP (A): 91.4530 49.4870 -15.3530 REMARK 3 T TENSOR REMARK 3 T11: 0.1487 T22: 0.0412 REMARK 3 T33: 0.2498 T12: 0.0696 REMARK 3 T13: 0.0072 T23: -0.0328 REMARK 3 L TENSOR REMARK 3 L11: 2.0282 L22: 0.8546 REMARK 3 L33: 5.2901 L12: 0.3067 REMARK 3 L13: -2.3687 L23: -0.1588 REMARK 3 S TENSOR REMARK 3 S11: 0.0591 S12: 0.0538 S13: -0.1590 REMARK 3 S21: -0.0339 S22: -0.0527 S23: -0.0926 REMARK 3 S31: 0.0766 S32: 0.0067 S33: -0.0064 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 1 E 5 REMARK 3 ORIGIN FOR THE GROUP (A): 92.7540 56.0270 -0.7570 REMARK 3 T TENSOR REMARK 3 T11: 0.2919 T22: 0.3076 REMARK 3 T33: 0.2810 T12: 0.0104 REMARK 3 T13: -0.0646 T23: -0.0480 REMARK 3 L TENSOR REMARK 3 L11: 4.0357 L22: 6.9577 REMARK 3 L33: 12.3830 L12: 3.8262 REMARK 3 L13: -5.1336 L23: -0.7430 REMARK 3 S TENSOR REMARK 3 S11: 0.5274 S12: -0.2813 S13: -0.1038 REMARK 3 S21: 0.9059 S22: -0.3119 S23: -0.4725 REMARK 3 S31: -0.3372 S32: 0.2815 S33: -0.2154 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.30 REMARK 3 ION PROBE RADIUS : 1.00 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 5H8W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000216674. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31168 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 37.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.67900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 45.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, VAPOR DIFFUSION, TEMPERATURE REMARK 280 280.55K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 118.55467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.27733 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 88.91600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.63867 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 148.19333 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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 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 GLN A 20 CG CD OE1 NE2 REMARK 470 GLN A 481 CG CD OE1 NE2 REMARK 470 DA E 5 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DA E 5 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA E 5 C2 N3 C4 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 DT E 1 P DT E 1 OP3 -0.118 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 SER A 29 148.46 -173.51 REMARK 500 LEU A 148 70.19 47.32 REMARK 500 ASP A 245 58.20 38.47 REMARK 500 GLN A 250 94.38 -22.44 REMARK 500 HIS A 495 177.09 66.53 REMARK 500 LYS A 547 52.60 -140.91 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 SF4 A 801 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 92 SG REMARK 620 2 SF4 A 801 S1 119.5 REMARK 620 3 SF4 A 801 S2 117.0 103.6 REMARK 620 4 SF4 A 801 S4 107.6 102.2 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 801 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 113 SG REMARK 620 2 SF4 A 801 S1 115.5 REMARK 620 3 SF4 A 801 S3 122.2 103.3 REMARK 620 4 SF4 A 801 S4 105.9 102.9 104.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 801 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 128 SG REMARK 620 2 SF4 A 801 S1 126.1 REMARK 620 3 SF4 A 801 S2 103.6 103.9 REMARK 620 4 SF4 A 801 S3 115.2 103.4 101.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 802 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 162 OD1 REMARK 620 2 HOH A 914 O 95.7 REMARK 620 3 HOH A 908 O 96.4 104.8 REMARK 620 4 GLU A 312 OE1 62.0 139.6 50.9 REMARK 620 5 GLU A 315 OE1 62.2 140.1 51.0 0.5 REMARK 620 6 HOH A 907 O 160.4 103.4 83.2 104.3 104.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 801 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 164 SG REMARK 620 2 SF4 A 801 S2 113.7 REMARK 620 3 SF4 A 801 S3 113.6 102.8 REMARK 620 4 SF4 A 801 S4 114.5 105.9 105.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 803 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 921 O REMARK 620 2 HOH A 917 O 90.6 REMARK 620 3 HOH A 941 O 176.0 92.9 REMARK 620 4 HOH A 902 O 91.8 87.7 90.2 REMARK 620 5 HOH A 909 O 82.8 171.8 93.9 87.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 803 DBREF 5H8W A 19 615 UNP Q9HM14 XPD_THEAC 1 597 DBREF 5H8W E 1 5 PDB 5H8W 5H8W 1 5 SEQADV 5H8W ALA A 306 UNP Q9HM14 TYR 288 ENGINEERED MUTATION SEQADV 5H8W ALA A 329 UNP Q9HM14 CYS 311 ENGINEERED MUTATION SEQADV 5H8W ALA A 363 UNP Q9HM14 CYS 345 ENGINEERED MUTATION SEQADV 5H8W CYS A 542 UNP Q9HM14 GLU 524 ENGINEERED MUTATION SEQADV 5H8W ALA A 578 UNP Q9HM14 CYS 560 ENGINEERED MUTATION SEQRES 1 A 597 MET GLN LYS SER TYR GLY VAL ALA LEU GLU SER PRO THR SEQRES 2 A 597 GLY SER GLY LYS THR ILE MET ALA LEU LYS SER ALA LEU SEQRES 3 A 597 GLN TYR SER SER GLU ARG LYS LEU LYS VAL LEU TYR LEU SEQRES 4 A 597 VAL ARG THR ASN SER GLN GLU GLU GLN VAL ILE LYS GLU SEQRES 5 A 597 LEU ARG SER LEU SER SER THR MET LYS ILE ARG ALA ILE SEQRES 6 A 597 PRO MET GLN GLY ARG VAL ASN MET CYS ILE LEU TYR ARG SEQRES 7 A 597 MET VAL ASP ASP LEU HIS GLU ILE ASN ALA GLU SER LEU SEQRES 8 A 597 ALA LYS PHE CYS ASN MET LYS LYS ARG GLU VAL MET ALA SEQRES 9 A 597 GLY ASN GLU ALA ALA CYS PRO TYR PHE ASN PHE LYS ILE SEQRES 10 A 597 ARG SER ASP GLU THR LYS ARG PHE LEU PHE ASP GLU LEU SEQRES 11 A 597 PRO THR ALA GLU GLU PHE TYR ASP TYR GLY GLU ARG ASN SEQRES 12 A 597 ASN VAL CYS PRO TYR GLU SER MET LYS ALA ALA LEU PRO SEQRES 13 A 597 ASP ALA ASP ILE VAL ILE ALA PRO TYR ALA TYR PHE LEU SEQRES 14 A 597 ASN ARG SER VAL ALA GLU LYS PHE LEU SER HIS TRP GLY SEQRES 15 A 597 VAL SER ARG ASN GLN ILE VAL ILE ILE LEU ASP GLU ALA SEQRES 16 A 597 HIS ASN LEU PRO ASP ILE GLY ARG SER ILE GLY SER PHE SEQRES 17 A 597 ARG ILE SER VAL GLU SER LEU ASN ARG ALA ASP ARG GLU SEQRES 18 A 597 ALA GLN ALA TYR GLY ASP PRO GLU LEU SER GLN LYS ILE SEQRES 19 A 597 HIS VAL SER ASP LEU ILE GLU MET ILE ARG SER ALA LEU SEQRES 20 A 597 GLN SER MET VAL SER GLU ARG CYS GLY LYS GLY ASP VAL SEQRES 21 A 597 ARG ILE ARG PHE GLN GLU PHE MET GLU TYR MET ARG ILE SEQRES 22 A 597 MET ASN LYS ARG SER GLU ARG GLU ILE ARG SER LEU LEU SEQRES 23 A 597 ASN ALA LEU TYR LEU PHE GLY GLU TYR VAL GLU ASN GLU SEQRES 24 A 597 LYS GLU LYS VAL GLY LYS VAL PRO PHE SER TYR ALA SER SEQRES 25 A 597 SER VAL ALA SER ARG ILE ILE ALA PHE SER ASP GLN ASP SEQRES 26 A 597 GLU GLU LYS TYR ALA ALA ILE LEU SER PRO GLU ASP GLY SEQRES 27 A 597 GLY TYR MET GLN ALA ALA ALA LEU ASP PRO SER GLY ILE SEQRES 28 A 597 LEU GLU VAL LEU LYS GLU SER LYS THR ILE HIS MET SER SEQRES 29 A 597 GLY THR LEU ASP PRO PHE ASP PHE TYR SER ASP ILE THR SEQRES 30 A 597 GLY PHE GLU ILE PRO PHE LYS LYS ILE GLY GLU ILE PHE SEQRES 31 A 597 PRO PRO GLU ASN ARG TYR ILE ALA TYR TYR ASP GLY VAL SEQRES 32 A 597 SER SER LYS TYR ASP THR LEU ASP GLU LYS GLU LEU ASP SEQRES 33 A 597 ARG MET ALA THR VAL ILE GLU ASP ILE ILE LEU LYS VAL SEQRES 34 A 597 LYS LYS ASN THR ILE VAL TYR PHE PRO SER TYR SER LEU SEQRES 35 A 597 MET ASP ARG VAL GLU ASN ARG VAL SER PHE GLU HIS MET SEQRES 36 A 597 LYS GLU TYR ARG GLY ILE ASP GLN LYS GLU LEU TYR SER SEQRES 37 A 597 MET LEU LYS LYS PHE ARG ARG ASP HIS GLY THR ILE PHE SEQRES 38 A 597 ALA VAL SER GLY GLY ARG LEU SER GLU GLY ILE ASN PHE SEQRES 39 A 597 PRO GLY ASN GLU LEU GLU MET ILE ILE LEU ALA GLY LEU SEQRES 40 A 597 PRO PHE PRO ARG PRO ASP ALA ILE ASN ARG SER LEU PHE SEQRES 41 A 597 ASP TYR TYR CYS ARG LYS TYR GLY LYS GLY TRP GLU TYR SEQRES 42 A 597 SER VAL VAL TYR PRO THR ALA ILE LYS ILE ARG GLN GLU SEQRES 43 A 597 ILE GLY ARG LEU ILE ARG SER ALA GLU ASP THR GLY ALA SEQRES 44 A 597 ALA VAL ILE LEU ASP LYS ARG ALA GLY GLN PHE ARG LYS SEQRES 45 A 597 PHE ILE PRO ASP MET LYS LYS THR SER ASP PRO ALA SER SEQRES 46 A 597 ASP ILE TYR ASN PHE PHE ILE SER ALA GLN ALA ARG SEQRES 1 E 5 DT DA DC DG DA HET SF4 A 801 8 HET NA A 802 1 HET NA A 803 1 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM NA SODIUM ION FORMUL 3 SF4 FE4 S4 FORMUL 4 NA 2(NA 1+) FORMUL 6 HOH *43(H2 O) HELIX 1 AA1 SER A 33 ARG A 50 1 18 HELIX 2 AA2 THR A 60 MET A 78 1 19 HELIX 3 AA3 GLY A 87 CYS A 92 1 6 HELIX 4 AA4 ILE A 93 ASP A 99 1 7 HELIX 5 AA5 ASN A 105 ALA A 122 1 18 HELIX 6 AA6 ASN A 132 ARG A 136 5 5 HELIX 7 AA7 SER A 137 LEU A 148 1 12 HELIX 8 AA8 THR A 150 ASN A 162 1 13 HELIX 9 AA9 CYS A 164 LEU A 173 1 10 HELIX 10 AB1 PRO A 174 ALA A 176 5 3 HELIX 11 AB2 TYR A 183 LEU A 187 1 5 HELIX 12 AB3 ASN A 188 GLY A 200 1 13 HELIX 13 AB4 SER A 202 ASN A 204 5 3 HELIX 14 AB5 GLU A 212 HIS A 214 5 3 HELIX 15 AB6 ASN A 215 SER A 225 1 11 HELIX 16 AB7 VAL A 230 TYR A 243 1 14 HELIX 17 AB8 VAL A 254 CYS A 273 1 20 HELIX 18 AB9 PHE A 282 LYS A 294 1 13 HELIX 19 AC1 SER A 296 VAL A 321 1 26 HELIX 20 AC2 SER A 327 ASP A 341 1 15 HELIX 21 AC3 PRO A 366 GLU A 371 1 6 HELIX 22 AC4 VAL A 372 SER A 376 5 5 HELIX 23 AC5 PRO A 387 GLY A 396 1 10 HELIX 24 AC6 PRO A 409 GLU A 411 5 3 HELIX 25 AC7 LYS A 424 LEU A 428 5 5 HELIX 26 AC8 ASP A 429 LYS A 448 1 20 HELIX 27 AC9 SER A 457 ASN A 466 1 10 HELIX 28 AD1 ASP A 480 HIS A 495 1 16 HELIX 29 AD2 PRO A 513 LEU A 517 5 5 HELIX 30 AD3 ASP A 531 GLY A 546 1 16 HELIX 31 AD4 LYS A 547 VAL A 553 1 7 HELIX 32 AD5 VAL A 553 ARG A 567 1 15 HELIX 33 AD6 LYS A 583 ARG A 589 5 7 HELIX 34 AD7 ASP A 600 ARG A 615 1 16 SHEET 1 AA1 7 ALA A 82 PRO A 84 0 SHEET 2 AA1 7 ILE A 178 PRO A 182 1 O ILE A 180 N ILE A 83 SHEET 3 AA1 7 LYS A 53 VAL A 58 1 N TYR A 56 O VAL A 179 SHEET 4 AA1 7 ILE A 206 LEU A 210 1 O ILE A 209 N LEU A 57 SHEET 5 AA1 7 LYS A 377 SER A 382 1 O LYS A 377 N ILE A 208 SHEET 6 AA1 7 GLY A 24 GLU A 28 1 N LEU A 27 O HIS A 380 SHEET 7 AA1 7 PHE A 401 LYS A 402 1 O LYS A 402 N GLU A 28 SHEET 1 AA2 4 PHE A 226 SER A 229 0 SHEET 2 AA2 4 TYR A 358 ALA A 363 -1 O ALA A 361 N PHE A 226 SHEET 3 AA2 4 TYR A 347 SER A 352 -1 N ILE A 350 O GLN A 360 SHEET 4 AA2 4 VAL A 278 ILE A 280 -1 N VAL A 278 O LEU A 351 SHEET 1 AA3 2 GLU A 247 SER A 249 0 SHEET 2 AA3 2 ILE A 252 HIS A 253 -1 O ILE A 252 N LEU A 248 SHEET 1 AA4 7 MET A 473 LYS A 474 0 SHEET 2 AA4 7 THR A 497 VAL A 501 1 O THR A 497 N MET A 473 SHEET 3 AA4 7 THR A 451 PHE A 455 1 N VAL A 453 O ILE A 498 SHEET 4 AA4 7 MET A 519 LEU A 522 1 O ILE A 521 N TYR A 454 SHEET 5 AA4 7 GLY A 576 LEU A 581 1 O LEU A 581 N LEU A 522 SHEET 6 AA4 7 ARG A 413 TYR A 418 1 N TYR A 418 O ILE A 580 SHEET 7 AA4 7 LYS A 596 LYS A 597 1 O LYS A 596 N ILE A 415 LINK SG CYS A 92 FE3 SF4 A 801 1555 1555 2.30 LINK SG CYS A 113 FE2 SF4 A 801 1555 1555 2.31 LINK SG CYS A 128 FE4 SF4 A 801 1555 1555 2.33 LINK OD1 ASN A 162 NA NA A 802 1555 1555 2.24 LINK SG CYS A 164 FE1 SF4 A 801 1555 1555 2.25 LINK NA NA A 802 O HOH A 914 1555 1555 2.03 LINK NA NA A 802 O HOH A 908 1555 1555 2.19 LINK NA NA A 803 O HOH A 921 1555 1555 2.21 LINK NA NA A 803 O HOH A 917 1555 1555 2.19 LINK NA NA A 803 O HOH A 941 1555 1555 2.00 LINK OE1 GLU A 312 NA NA A 802 1555 5565 2.35 LINK OE1 GLU A 315 NA NA A 802 1555 5565 2.31 LINK NA NA A 802 O HOH A 907 1555 6654 2.04 LINK NA NA A 803 O HOH A 902 1555 5675 2.14 LINK NA NA A 803 O HOH A 909 1555 5675 2.26 CISPEP 1 ASP A 386 PRO A 387 0 4.79 SITE 1 AC1 5 ARG A 88 CYS A 92 CYS A 113 CYS A 128 SITE 2 AC1 5 CYS A 164 SITE 1 AC2 7 GLU A 159 ASN A 162 GLU A 312 GLU A 315 SITE 2 AC2 7 HOH A 907 HOH A 908 HOH A 914 SITE 1 AC3 5 HOH A 902 HOH A 909 HOH A 917 HOH A 921 SITE 2 AC3 5 HOH A 941 CRYST1 78.569 78.569 177.832 90.00 90.00 120.00 P 65 6 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 0.012728 0.007348 0.000000 0.00000 SCALE2 0.000000 0.014697 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005623 0.00000