HEADER DNA BINDING PROTEIN/DNA 26-MAY-15 5BNH TITLE CRYSTAL STRUCTURE OF THE HLTF HIRAN DOMAIN WITH A SSDNA FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*(GD)P*GP*TP*G)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*(TD)P*TP*G)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HELICASE-LIKE TRANSCRIPTION FACTOR; COMPND 11 CHAIN: A, D; COMPND 12 FRAGMENT: UNP RESIDUES 55-175; COMPND 13 SYNONYM: DNA-BINDING PROTEIN/PLASMINOGEN ACTIVATOR INHIBITOR 1 COMPND 14 REGULATOR,HIP116,RING FINGER PROTEIN 80,SWI/SNF-RELATED MATRIX- COMPND 15 ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY A MEMBER COMPND 16 3,SUCROSE NONFERMENTING PROTEIN 2-LIKE 3; COMPND 17 EC: 3.6.4.-,6.3.2.-; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: HLTF; SOURCE 14 EXPRESSION_SYSTEM: ENTEROBACTERIA PHAGE L1; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 268588 KEYWDS DNA DAMAGE, DNA RECOGNITION, DNA BINDING DOMAIN, DNA BINDING PROTEIN- KEYWDS 2 DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.NECULAI,J.R.WALKER,J.WEIGELT,C.BOUNTRA,A.M.EDWARDS,C.H.ARROWSMITH, AUTHOR 2 S.DHE-PAGANON REVDAT 2 20-MAR-24 5BNH 1 REMARK LINK REVDAT 1 25-MAY-16 5BNH 0 JRNL AUTH D.NECULAI,J.R.WALKER,J.WEIGELT,C.BOUNTRA,A.M.EDWARDS, JRNL AUTH 2 C.H.ARROWSMITH,S.DHE-PAGANON JRNL TITL CO-CRYSTAL STRUCTURE OF THE HLTF HIRAN DOMAIN WITH A SSDNA JRNL TITL 2 FRAGMENT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 26849 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1414 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1945 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1898 REMARK 3 NUCLEIC ACID ATOMS : 96 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 148 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.35000 REMARK 3 B22 (A**2) : -1.48000 REMARK 3 B33 (A**2) : 0.13000 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): 0.099 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.137 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2063 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1947 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2801 ; 1.933 ; 1.912 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4464 ; 0.906 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 244 ; 6.714 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;35.637 ;25.217 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 326 ;13.601 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;26.306 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 294 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2322 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 478 ; 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): 986 ; 1.843 ; 1.533 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 981 ; 1.716 ; 1.524 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1224 ; 2.583 ; 2.277 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1225 ; 2.583 ; 2.277 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1077 ; 3.691 ; 2.072 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1070 ; 3.651 ; 2.053 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1566 ; 5.585 ; 2.898 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2343 ; 7.737 ;14.604 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2295 ; 7.615 ;14.247 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 : 4 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 53 A 175 REMARK 3 ORIGIN FOR THE GROUP (A): 5.4193 -13.7611 -8.5797 REMARK 3 T TENSOR REMARK 3 T11: 0.0178 T22: 0.0404 REMARK 3 T33: 0.0422 T12: -0.0057 REMARK 3 T13: 0.0131 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 0.2564 L22: 0.3657 REMARK 3 L33: 0.2014 L12: -0.1963 REMARK 3 L13: -0.1313 L23: -0.0532 REMARK 3 S TENSOR REMARK 3 S11: 0.0041 S12: 0.0117 S13: -0.0373 REMARK 3 S21: 0.0074 S22: 0.0042 S23: 0.0348 REMARK 3 S31: -0.0289 S32: -0.0018 S33: -0.0083 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 : B 1 B 3 REMARK 3 ORIGIN FOR THE GROUP (A): 0.9577 -3.6297 3.2442 REMARK 3 T TENSOR REMARK 3 T11: 0.1194 T22: 0.0224 REMARK 3 T33: 0.0605 T12: -0.0373 REMARK 3 T13: 0.0728 T23: -0.0096 REMARK 3 L TENSOR REMARK 3 L11: 6.5828 L22: 0.3532 REMARK 3 L33: 7.9925 L12: 0.4633 REMARK 3 L13: 2.3761 L23: 1.6797 REMARK 3 S TENSOR REMARK 3 S11: 0.6119 S12: -0.3833 S13: 0.1357 REMARK 3 S21: -0.0990 S22: -0.0212 S23: -0.1264 REMARK 3 S31: -0.4492 S32: -0.1198 S33: -0.5907 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 : C 1 C 3 REMARK 3 ORIGIN FOR THE GROUP (A): 32.1508 -43.4316 -16.0556 REMARK 3 T TENSOR REMARK 3 T11: 0.0320 T22: 0.0450 REMARK 3 T33: 0.0477 T12: 0.0163 REMARK 3 T13: 0.0208 T23: 0.0076 REMARK 3 L TENSOR REMARK 3 L11: 1.8569 L22: 8.0277 REMARK 3 L33: 4.9675 L12: 3.5342 REMARK 3 L13: 0.2342 L23: -2.0870 REMARK 3 S TENSOR REMARK 3 S11: -0.1978 S12: 0.0018 S13: -0.0494 REMARK 3 S21: -0.4345 S22: 0.0239 S23: -0.1854 REMARK 3 S31: 0.1004 S32: -0.0239 S33: 0.1739 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 : D 53 D 175 REMARK 3 ORIGIN FOR THE GROUP (A): 19.0181 -37.3846 -11.4873 REMARK 3 T TENSOR REMARK 3 T11: 0.0114 T22: 0.0403 REMARK 3 T33: 0.0390 T12: 0.0023 REMARK 3 T13: 0.0138 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.3973 L22: 0.3258 REMARK 3 L33: 0.5412 L12: -0.0106 REMARK 3 L13: -0.3454 L23: 0.0852 REMARK 3 S TENSOR REMARK 3 S11: -0.0024 S12: 0.0175 S13: 0.0137 REMARK 3 S21: -0.0237 S22: 0.0181 S23: 0.0303 REMARK 3 S31: 0.0133 S32: 0.0128 S33: -0.0157 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5BNH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000210205. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97921 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28334 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 51.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.9000 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: 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 (%): 45.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE TRIHYDRATE PH REMARK 280 5.0, 40% 2-METHYL-2,4-PENTANEDIOL, EVAPORATION, TEMPERATURE 291K 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 24.23450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.38150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.05850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.38150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.23450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.05850 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, A, 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 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 DG B 1 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG B 1 C2 N2 N3 C4 REMARK 470 DT C 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DT C 1 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT C 1 C7 C6 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 O ACT D 203 O HOH D 301 1.45 REMARK 500 O HOH A 359 O HOH A 375 1.47 REMARK 500 OXT ACT D 203 O HOH D 302 1.48 REMARK 500 O HOH A 303 O HOH A 310 1.93 REMARK 500 O2 PO4 A 203 O HOH A 301 2.01 REMARK 500 O HOH A 352 O HOH A 363 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 301 O HOH A 361 4445 1.96 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 GLU A 81 CD GLU A 81 OE2 0.071 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 64 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG D 71 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG D 71 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP D 88 CB - CG - OD2 ANGL. DEV. = -5.8 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 94 106.85 -169.86 REMARK 500 ASP D 56 -23.04 103.60 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 VAL A 55 ASP A 56 -34.95 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 NA A 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 70 O REMARK 620 2 TYR A 73 O 92.8 REMARK 620 3 HOH A 335 O 88.4 93.0 REMARK 620 4 HOH A 365 O 86.2 154.4 112.5 REMARK 620 5 HOH A 370 O 169.8 96.5 87.0 87.2 REMARK 620 6 HOH A 373 O 92.1 89.1 177.9 65.5 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 107 OE1 REMARK 620 2 PO4 A 203 O4 124.6 REMARK 620 3 HOH A 331 O 116.2 117.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT D 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT D 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT D 204 DBREF 5BNH B 1 3 PDB 5BNH 5BNH 1 3 DBREF 5BNH C 1 3 PDB 5BNH 5BNH 1 3 DBREF 5BNH A 55 175 UNP Q14527 HLTF_HUMAN 55 175 DBREF 5BNH D 55 175 UNP Q14527 HLTF_HUMAN 55 175 SEQADV 5BNH GLY A 53 UNP Q14527 EXPRESSION TAG SEQADV 5BNH SER A 54 UNP Q14527 EXPRESSION TAG SEQADV 5BNH GLY D 53 UNP Q14527 EXPRESSION TAG SEQADV 5BNH SER D 54 UNP Q14527 EXPRESSION TAG SEQRES 1 B 3 DG DT DG SEQRES 1 C 3 DT DT DG SEQRES 1 A 123 GLY SER VAL ASP SER VAL LEU PHE GLY SER LEU ARG GLY SEQRES 2 A 123 HIS VAL VAL GLY LEU ARG TYR TYR THR GLY VAL VAL ASN SEQRES 3 A 123 ASN ASN GLU MET VAL ALA LEU GLN ARG ASP PRO ASN ASN SEQRES 4 A 123 PRO TYR ASP LYS ASN ALA ILE LYS VAL ASN ASN VAL ASN SEQRES 5 A 123 GLY ASN GLN VAL GLY HIS LEU LYS LYS GLU LEU ALA GLY SEQRES 6 A 123 ALA LEU ALA TYR ILE MET ASP ASN LYS LEU ALA GLN ILE SEQRES 7 A 123 GLU GLY VAL VAL PRO PHE GLY ALA ASN ASN ALA PHE THR SEQRES 8 A 123 MET PRO LEU HIS MET THR PHE TRP GLY LYS GLU GLU ASN SEQRES 9 A 123 ARG LYS ALA VAL SER ASP GLN LEU LYS LYS HIS GLY PHE SEQRES 10 A 123 LYS LEU GLY PRO ALA PRO SEQRES 1 D 123 GLY SER VAL ASP SER VAL LEU PHE GLY SER LEU ARG GLY SEQRES 2 D 123 HIS VAL VAL GLY LEU ARG TYR TYR THR GLY VAL VAL ASN SEQRES 3 D 123 ASN ASN GLU MET VAL ALA LEU GLN ARG ASP PRO ASN ASN SEQRES 4 D 123 PRO TYR ASP LYS ASN ALA ILE LYS VAL ASN ASN VAL ASN SEQRES 5 D 123 GLY ASN GLN VAL GLY HIS LEU LYS LYS GLU LEU ALA GLY SEQRES 6 D 123 ALA LEU ALA TYR ILE MET ASP ASN LYS LEU ALA GLN ILE SEQRES 7 D 123 GLU GLY VAL VAL PRO PHE GLY ALA ASN ASN ALA PHE THR SEQRES 8 D 123 MET PRO LEU HIS MET THR PHE TRP GLY LYS GLU GLU ASN SEQRES 9 D 123 ARG LYS ALA VAL SER ASP GLN LEU LYS LYS HIS GLY PHE SEQRES 10 D 123 LYS LEU GLY PRO ALA PRO HET NA A 201 1 HET NA A 202 1 HET PO4 A 203 5 HET PO4 A 204 5 HET ACT D 201 4 HET ACT D 202 4 HET ACT D 203 4 HET ACT D 204 4 HETNAM NA SODIUM ION HETNAM PO4 PHOSPHATE ION HETNAM ACT ACETATE ION FORMUL 5 NA 2(NA 1+) FORMUL 7 PO4 2(O4 P 3-) FORMUL 9 ACT 4(C2 H3 O2 1-) FORMUL 13 HOH *148(H2 O) HELIX 1 AA1 GLY A 69 TYR A 73 5 5 HELIX 2 AA2 LYS A 112 ASN A 125 1 14 HELIX 3 AA3 LYS A 153 GLU A 155 5 3 HELIX 4 AA4 ASN A 156 LYS A 166 1 11 HELIX 5 AA5 GLY D 69 TYR D 73 5 5 HELIX 6 AA6 LYS D 112 ASN D 125 1 14 HELIX 7 AA7 LYS D 153 GLU D 155 5 3 HELIX 8 AA8 ASN D 156 HIS D 167 1 12 SHEET 1 AA1 7 VAL A 58 VAL A 68 0 SHEET 2 AA1 7 GLN A 107 LEU A 111 -1 O HIS A 110 N VAL A 68 SHEET 3 AA1 7 ILE A 98 ASN A 101 -1 N VAL A 100 O VAL A 108 SHEET 4 AA1 7 GLU A 81 ARG A 87 -1 N ALA A 84 O ASN A 101 SHEET 5 AA1 7 GLN A 129 VAL A 134 -1 O VAL A 134 N GLU A 81 SHEET 6 AA1 7 MET A 144 GLY A 152 -1 O HIS A 147 N VAL A 133 SHEET 7 AA1 7 VAL A 58 VAL A 68 -1 N LEU A 63 O MET A 148 SHEET 1 AA2 7 VAL D 58 VAL D 68 0 SHEET 2 AA2 7 GLN D 107 LEU D 111 -1 O HIS D 110 N VAL D 68 SHEET 3 AA2 7 ILE D 98 ASN D 101 -1 N VAL D 100 O VAL D 108 SHEET 4 AA2 7 MET D 82 ARG D 87 -1 N GLN D 86 O LYS D 99 SHEET 5 AA2 7 GLN D 129 VAL D 133 -1 O GLY D 132 N VAL D 83 SHEET 6 AA2 7 MET D 144 GLY D 152 -1 O THR D 149 N GLU D 131 SHEET 7 AA2 7 VAL D 58 VAL D 68 -1 N VAL D 67 O MET D 144 LINK O LEU A 70 NA NA A 201 1555 1555 2.40 LINK O TYR A 73 NA NA A 201 1555 1555 2.26 LINK OE1 GLN A 107 NA NA A 202 1555 1555 2.73 LINK NA NA A 201 O HOH A 335 1555 1555 2.23 LINK NA NA A 201 O HOH A 365 1555 1555 2.08 LINK NA NA A 201 O HOH A 370 1555 1555 2.35 LINK NA NA A 201 O HOH A 373 1555 1555 2.61 LINK NA NA A 202 O4 PO4 A 203 1555 1555 2.76 LINK NA NA A 202 O HOH A 331 1555 4445 2.83 CISPEP 1 ALA A 174 PRO A 175 0 -9.58 CISPEP 2 ALA D 174 PRO D 175 0 -10.35 SITE 1 AC1 6 LEU A 70 TYR A 73 HOH A 335 HOH A 365 SITE 2 AC1 6 HOH A 370 HOH A 373 SITE 1 AC2 4 HIS A 66 GLN A 107 PO4 A 203 HOH A 331 SITE 1 AC3 9 GLY A 65 HIS A 66 GLY A 105 ASN A 106 SITE 2 AC3 9 GLN A 107 NA A 202 HOH A 301 HOH A 303 SITE 3 AC3 9 HOH A 326 SITE 1 AC4 5 ARG A 64 HIS A 147 HOH A 307 DT B 2 SITE 2 AC4 5 DG B 3 SITE 1 AC5 4 ASN D 140 ALA D 141 PHE D 142 THR D 143 SITE 1 AC6 4 ASN D 79 GLY D 137 ALA D 138 ASN D 139 SITE 1 AC7 7 VAL A 76 GLU A 81 ASN A 104 GLN D 163 SITE 2 AC7 7 HIS D 167 HOH D 301 HOH D 302 SITE 1 AC8 6 GLY D 65 HIS D 66 LYS D 112 LYS D 158 SITE 2 AC8 6 HOH D 312 HOH D 337 CRYST1 48.469 50.117 102.763 90.00 90.00 90.00 P 21 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 0.020632 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019953 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009731 0.00000