PDB Short entry for 5PXU HEADER TRANSCRIPTION 08-FEB-17 5PXU TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF SP100 AFTER TITLE 2 INITIAL REFINEMENT WITH NO LIGAND MODELLED (STRUCTURE 54) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR AUTOANTIGEN SP-100; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NUCLEAR DOT-ASSOCIATED SP100 PROTEIN,SPECKLED 100 KDA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SP100; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PANDDA, SGC - DIAMOND I04-1 FRAGMENT SCREENING, BROMODOMAIN, KEYWDS 2 EPIGENETICS, XCHEMEXPLORER, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR N.M.PEARCE,T.KROJER,R.TALON,A.R.BRADLEY,M.FAIRHEAD,R.SETHI,N.WRIGHT, AUTHOR 2 E.MACLEAN,P.COLLINS,J.BRANDAO-NETO,A.DOUANGAMATH,Z.RENJIE,A.DIAS, AUTHOR 3 J.NG,P.E.BRENNAN,O.COX,C.BOUNTRA,C.H.ARROWSMITH,A.EDWARDS,F.VON AUTHOR 4 DELFT REVDAT 3 06-MAR-24 5PXU 1 REMARK REVDAT 2 04-OCT-17 5PXU 1 JRNL REMARK REVDAT 1 22-MAR-17 5PXU 0 JRNL AUTH N.M.PEARCE,T.KROJER,A.R.BRADLEY,P.COLLINS,R.P.NOWAK,R.TALON, JRNL AUTH 2 B.D.MARSDEN,S.KELM,J.SHI,C.M.DEANE,F.VON DELFT JRNL TITL A MULTI-CRYSTAL METHOD FOR EXTRACTING OBSCURED JRNL TITL 2 CRYSTALLOGRAPHIC STATES FROM CONVENTIONALLY UNINTERPRETABLE JRNL TITL 3 ELECTRON DENSITY. JRNL REF NAT COMMUN V. 8 15123 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 28436492 JRNL DOI 10.1038/NCOMMS15123 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 41581 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) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.302 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2143 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3109 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 177 REMARK 3 BIN FREE R VALUE : 0.3740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2925 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 579 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.93000 REMARK 3 B22 (A**2) : 2.49000 REMARK 3 B33 (A**2) : -1.45000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.159 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.163 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.144 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.930 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3125 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2888 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4223 ; 1.739 ; 1.936 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6681 ; 1.038 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 386 ; 6.446 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;37.785 ;24.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 574 ;13.378 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.483 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 433 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3560 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 792 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1452 ; 3.078 ; 3.008 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1451 ; 3.076 ; 3.003 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1820 ; 4.964 ; 4.494 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5PXU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1001401248. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9200 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43724 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 40.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.76300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 4PTB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH 6.1 -- 20% PEG20K, PH 7, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 63.87000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.70500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 63.87000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.70500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLU A 700 REMARK 465 LYS A 879 REMARK 465 THR B 877 REMARK 465 SER B 878 REMARK 465 LYS B 879 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 737 CG CD CE NZ REMARK 470 GLU B 700 CG CD OE1 OE2 REMARK 470 GLU B 756 CG CD OE1 OE2 REMARK 470 SER B 757 OG REMARK 470 GLN B 758 CG CD OE1 NE2 REMARK 470 SER B 759 OG REMARK 470 ARG B 803 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 804 CG CD OE1 OE2 REMARK 470 SER B 806 OG REMARK 470 GLN B 807 CG CD OE1 NE2 REMARK 470 GLU B 876 CG CD OE1 OE2 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 HOH A 1125 O HOH A 1238 1.99 REMARK 500 NH1 ARG A 829 O HOH A 1001 2.05 REMARK 500 O HOH B 1024 O HOH B 1050 2.11 REMARK 500 O2 EDO B 903 O HOH B 1001 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 GLU A 763 CD GLU A 763 OE1 -0.074 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 869 NE - CZ - NH1 ANGL. DEV. = 3.1 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 ASN A 736 -112.93 -100.04 REMARK 500 LYS A 737 96.10 62.16 REMARK 500 ARG A 849 -122.70 55.68 REMARK 500 ASN B 738 106.92 -175.39 REMARK 500 PRO B 755 99.83 -61.38 REMARK 500 SER B 757 -163.37 -61.32 REMARK 500 GLN B 758 33.23 -68.36 REMARK 500 TYR B 801 -100.92 -114.85 REMARK 500 ASN B 802 72.96 -112.64 REMARK 500 GLU B 804 -109.06 -129.15 REMARK 500 ARG B 849 -111.97 45.22 REMARK 500 GLN B 875 136.84 -33.08 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 PRO B 755 GLU B 756 146.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1313 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH B1264 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH B1265 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH B1266 DISTANCE = 7.06 ANGSTROMS 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 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 705 SG REMARK 620 2 CYS A 708 SG 106.3 REMARK 620 3 HIS A 725 ND1 103.6 98.0 REMARK 620 4 CYS A 728 SG 107.4 118.1 121.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 717 SG REMARK 620 2 CYS A 720 SG 115.1 REMARK 620 3 CYS A 742 SG 107.9 106.3 REMARK 620 4 CYS A 745 SG 109.8 101.3 116.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 903 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 754 SG REMARK 620 2 GLU A 756 OE2 110.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 705 SG REMARK 620 2 CYS B 708 SG 111.1 REMARK 620 3 HIS B 725 ND1 113.9 93.5 REMARK 620 4 CYS B 728 SG 111.6 114.1 111.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 717 SG REMARK 620 2 CYS B 720 SG 114.8 REMARK 620 3 CYS B 742 SG 113.2 107.1 REMARK 620 4 CYS B 745 SG 104.2 107.5 109.9 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 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 903 DBREF 5PXU A 700 879 UNP P23497 SP100_HUMAN 700 879 DBREF 5PXU B 700 879 UNP P23497 SP100_HUMAN 700 879 SEQRES 1 A 180 GLU ASN SER ASN ILE CYS GLU VAL CYS ASN LYS TRP GLY SEQRES 2 A 180 ARG LEU PHE CYS CYS ASP THR CYS PRO ARG SER PHE HIS SEQRES 3 A 180 GLU HIS CYS HIS ILE PRO SER VAL GLU ALA ASN LYS ASN SEQRES 4 A 180 PRO TRP SER CYS ILE PHE CYS ARG ILE LYS THR ILE GLN SEQRES 5 A 180 GLU ARG CYS PRO GLU SER GLN SER GLY HIS GLN GLU SER SEQRES 6 A 180 GLU VAL LEU MET ARG GLN MET LEU PRO GLU GLU GLN LEU SEQRES 7 A 180 LYS CYS GLU PHE LEU LEU LEU LYS VAL TYR CYS ASP SER SEQRES 8 A 180 LYS SER CYS PHE PHE ALA SER GLU PRO TYR TYR ASN ARG SEQRES 9 A 180 GLU GLY SER GLN GLY PRO GLN LYS PRO MET TRP LEU ASN SEQRES 10 A 180 LYS VAL LYS THR SER LEU ASN GLU GLN MET TYR THR ARG SEQRES 11 A 180 VAL GLU GLY PHE VAL GLN ASP MET ARG LEU ILE PHE HIS SEQRES 12 A 180 ASN HIS LYS GLU PHE TYR ARG GLU ASP LYS PHE THR ARG SEQRES 13 A 180 LEU GLY ILE GLN VAL GLN ASP ILE PHE GLU LYS ASN PHE SEQRES 14 A 180 ARG ASN ILE PHE ALA ILE GLN GLU THR SER LYS SEQRES 1 B 180 GLU ASN SER ASN ILE CYS GLU VAL CYS ASN LYS TRP GLY SEQRES 2 B 180 ARG LEU PHE CYS CYS ASP THR CYS PRO ARG SER PHE HIS SEQRES 3 B 180 GLU HIS CYS HIS ILE PRO SER VAL GLU ALA ASN LYS ASN SEQRES 4 B 180 PRO TRP SER CYS ILE PHE CYS ARG ILE LYS THR ILE GLN SEQRES 5 B 180 GLU ARG CYS PRO GLU SER GLN SER GLY HIS GLN GLU SER SEQRES 6 B 180 GLU VAL LEU MET ARG GLN MET LEU PRO GLU GLU GLN LEU SEQRES 7 B 180 LYS CYS GLU PHE LEU LEU LEU LYS VAL TYR CYS ASP SER SEQRES 8 B 180 LYS SER CYS PHE PHE ALA SER GLU PRO TYR TYR ASN ARG SEQRES 9 B 180 GLU GLY SER GLN GLY PRO GLN LYS PRO MET TRP LEU ASN SEQRES 10 B 180 LYS VAL LYS THR SER LEU ASN GLU GLN MET TYR THR ARG SEQRES 11 B 180 VAL GLU GLY PHE VAL GLN ASP MET ARG LEU ILE PHE HIS SEQRES 12 B 180 ASN HIS LYS GLU PHE TYR ARG GLU ASP LYS PHE THR ARG SEQRES 13 B 180 LEU GLY ILE GLN VAL GLN ASP ILE PHE GLU LYS ASN PHE SEQRES 14 B 180 ARG ASN ILE PHE ALA ILE GLN GLU THR SER LYS HET ZN A 901 1 HET ZN A 902 1 HET ZN A 903 1 HET MES A 904 12 HET EDO A 905 4 HET ZN B 901 1 HET ZN B 902 1 HET EDO B 903 4 HETNAM ZN ZINC ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 5(ZN 2+) FORMUL 6 MES C6 H13 N O4 S FORMUL 7 EDO 2(C2 H6 O2) FORMUL 11 HOH *579(H2 O) HELIX 1 AA1 CYS A 742 CYS A 754 1 13 HELIX 2 AA2 PRO A 755 SER A 759 5 5 HELIX 3 AA3 GLN A 762 MET A 768 1 7 HELIX 4 AA4 LEU A 772 CYS A 788 1 17 HELIX 5 AA5 ASP A 789 LYS A 791 5 3 HELIX 6 AA6 SER A 792 SER A 797 1 6 HELIX 7 AA7 TRP A 814 GLU A 824 1 11 HELIX 8 AA8 ARG A 829 ARG A 849 1 21 HELIX 9 AA9 PHE A 853 PHE A 872 1 20 HELIX 10 AB1 CYS B 742 GLU B 752 1 11 HELIX 11 AB2 GLN B 762 MET B 768 1 7 HELIX 12 AB3 LEU B 772 CYS B 788 1 17 HELIX 13 AB4 ASP B 789 ALA B 796 5 8 HELIX 14 AB5 TRP B 814 GLU B 824 1 11 HELIX 15 AB6 ARG B 829 ARG B 849 1 21 HELIX 16 AB7 PHE B 853 PHE B 872 1 20 SHEET 1 AA1 2 PHE A 715 CYS A 716 0 SHEET 2 AA1 2 SER A 723 PHE A 724 -1 O PHE A 724 N PHE A 715 SHEET 1 AA2 2 PHE B 715 CYS B 716 0 SHEET 2 AA2 2 SER B 723 PHE B 724 -1 O PHE B 724 N PHE B 715 LINK SG CYS A 705 ZN ZN A 901 1555 1555 2.26 LINK SG CYS A 708 ZN ZN A 901 1555 1555 2.23 LINK SG CYS A 717 ZN ZN A 902 1555 1555 2.24 LINK SG CYS A 720 ZN ZN A 902 1555 1555 2.28 LINK ND1 HIS A 725 ZN ZN A 901 1555 1555 2.15 LINK SG CYS A 728 ZN ZN A 901 1555 1555 2.16 LINK SG CYS A 742 ZN ZN A 902 1555 1555 2.44 LINK SG CYS A 745 ZN ZN A 902 1555 1555 2.37 LINK SG ACYS A 754 ZN ZN A 903 1555 1555 3.00 LINK OE2 GLU A 756 ZN ZN A 903 1555 1555 2.36 LINK SG CYS B 705 ZN ZN B 901 1555 1555 2.40 LINK SG CYS B 708 ZN ZN B 901 1555 1555 2.33 LINK SG CYS B 717 ZN ZN B 902 1555 1555 2.30 LINK SG CYS B 720 ZN ZN B 902 1555 1555 2.38 LINK ND1 HIS B 725 ZN ZN B 901 1555 1555 2.20 LINK SG CYS B 728 ZN ZN B 901 1555 1555 2.21 LINK SG CYS B 742 ZN ZN B 902 1555 1555 2.26 LINK SG CYS B 745 ZN ZN B 902 1555 1555 2.20 CISPEP 1 ILE A 730 PRO A 731 0 -12.95 CISPEP 2 ASN A 738 PRO A 739 0 -2.75 CISPEP 3 ILE B 730 PRO B 731 0 -15.93 CISPEP 4 ASN B 738 PRO B 739 0 4.69 CISPEP 5 ARG B 803 GLU B 804 0 -6.16 SITE 1 AC1 4 CYS A 705 CYS A 708 HIS A 725 CYS A 728 SITE 1 AC2 4 CYS A 717 CYS A 720 CYS A 742 CYS A 745 SITE 1 AC3 2 CYS A 754 GLU A 756 SITE 1 AC4 12 ASN A 802 ARG A 803 TYR A 848 HOH A1052 SITE 2 AC4 12 HOH A1060 HOH A1073 HOH A1184 HOH A1238 SITE 3 AC4 12 ARG B 753 PRO B 773 GLU B 774 EDO B 903 SITE 1 AC5 6 GLU A 763 SER A 764 ARG A 838 HOH A1036 SITE 2 AC5 6 HOH A1098 HOH A1227 SITE 1 AC6 4 CYS B 705 CYS B 708 HIS B 725 CYS B 728 SITE 1 AC7 4 CYS B 717 CYS B 720 CYS B 742 CYS B 745 SITE 1 AC8 6 MES A 904 ARG B 746 HOH B1001 HOH B1010 SITE 2 AC8 6 HOH B1065 HOH B1108 CRYST1 127.740 45.410 83.310 90.00 102.33 90.00 C 1 2 1 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 0.007828 0.000000 0.001711 0.00000 SCALE2 0.000000 0.022022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012287 0.00000