HEADER SIGNALING PROTEIN 13-SEP-17 5YDK TITLE CRYSTAL STRUCTURE OF RNF168 UDM1 IN COMPLEX WITH LYS63-LINKED TITLE 2 DIUBIQUITIN, TETRAMERIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RNF168; COMPND 3 CHAIN: A, G, F, L; COMPND 4 FRAGMENT: UNP RESIDUES 113-194; COMPND 5 SYNONYM: HRNF168,RING FINGER PROTEIN 168,RING-TYPE E3 UBIQUITIN COMPND 6 TRANSFERASE RNF168; COMPND 7 EC: 2.3.2.27; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: UBIQUITIN-40S RIBOSOMAL PROTEIN S27A; COMPND 11 CHAIN: B, H, E, K; COMPND 12 FRAGMENT: UNP RESIDUES 1-76; COMPND 13 SYNONYM: UBIQUITIN CARBOXYL EXTENSION PROTEIN 80; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: UBIQUITIN-40S RIBOSOMAL PROTEIN S27A; COMPND 18 CHAIN: D, J, C, I; COMPND 19 FRAGMENT: UNP RESIDUES 1-76; COMPND 20 SYNONYM: UBIQUITIN CARBOXYL EXTENSION PROTEIN 80; COMPND 21 ENGINEERED: YES; COMPND 22 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RNF168; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: RPS27A, UBA80, UBCEP1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: RPS27A, UBA80, UBCEP1; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.S.TAKAHASHI,Y.SATO,S.FUKAI REVDAT 3 22-NOV-23 5YDK 1 LINK REVDAT 2 21-MAR-18 5YDK 1 TITLE REVDAT 1 07-MAR-18 5YDK 0 JRNL AUTH T.S.TAKAHASHI,Y.HIRADE,A.TOMA,Y.SATO,A.YAMAGATA,S.GOTO-ITO, JRNL AUTH 2 A.TOMITA,S.NAKADA,S.FUKAI JRNL TITL STRUCTURAL INSIGHTS INTO TWO DISTINCT BINDING MODULES FOR JRNL TITL 2 LYS63-LINKED POLYUBIQUITIN CHAINS IN RNF168 JRNL REF NAT COMMUN V. 9 170 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29330428 JRNL DOI 10.1038/S41467-017-02345-Y REMARK 2 REMARK 2 RESOLUTION. 2.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 40207 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2017 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.6601 - 6.0322 0.96 2825 159 0.1868 0.1957 REMARK 3 2 6.0322 - 4.7900 0.96 2717 155 0.1955 0.2121 REMARK 3 3 4.7900 - 4.1851 0.99 2813 130 0.1650 0.1917 REMARK 3 4 4.1851 - 3.8027 0.99 2797 138 0.1852 0.2168 REMARK 3 5 3.8027 - 3.5303 0.95 2676 137 0.2153 0.2657 REMARK 3 6 3.5303 - 3.3223 0.98 2755 146 0.2230 0.2460 REMARK 3 7 3.3223 - 3.1559 0.98 2745 146 0.2411 0.3188 REMARK 3 8 3.1559 - 3.0186 0.98 2716 165 0.2482 0.2827 REMARK 3 9 3.0186 - 2.9024 0.98 2711 164 0.2786 0.3126 REMARK 3 10 2.9024 - 2.8023 0.94 2627 136 0.3077 0.3280 REMARK 3 11 2.8023 - 2.7147 0.96 2732 132 0.3151 0.3477 REMARK 3 12 2.7147 - 2.6371 0.96 2722 126 0.3279 0.3619 REMARK 3 13 2.6371 - 2.5677 0.97 2657 142 0.3450 0.3653 REMARK 3 14 2.5677 - 2.5050 0.96 2697 141 0.3610 0.4122 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 7558 REMARK 3 ANGLE : 0.587 10120 REMARK 3 CHIRALITY : 0.042 1136 REMARK 3 PLANARITY : 0.003 1343 REMARK 3 DIHEDRAL : 20.845 4818 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5YDK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005075. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-15 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 : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40288 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12800 REMARK 200 FOR THE DATA SET : 6.8750 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.67300 REMARK 200 FOR SHELL : 1.250 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2FID REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 7.6 21% PEG3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 32.06000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H, J REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, E, C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, K, I 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 GLY A 108 REMARK 465 PRO A 109 REMARK 465 GLY A 110 REMARK 465 GLY A 192 REMARK 465 SER A 193 REMARK 465 ILE A 194 REMARK 465 GLY D 76 REMARK 465 ASP D 77 REMARK 465 GLY G 108 REMARK 465 PRO G 109 REMARK 465 GLY G 110 REMARK 465 HIS G 111 REMARK 465 GLY G 192 REMARK 465 SER G 193 REMARK 465 ILE G 194 REMARK 465 ARG J 74 REMARK 465 GLY J 75 REMARK 465 GLY J 76 REMARK 465 ASP J 77 REMARK 465 GLY F 108 REMARK 465 PRO F 109 REMARK 465 GLY F 192 REMARK 465 SER F 193 REMARK 465 ILE F 194 REMARK 465 ARG C 74 REMARK 465 GLY C 75 REMARK 465 GLY C 76 REMARK 465 ASP C 77 REMARK 465 GLY L 108 REMARK 465 PRO L 109 REMARK 465 GLY L 192 REMARK 465 SER L 193 REMARK 465 ILE L 194 REMARK 465 ARG I 74 REMARK 465 GLY I 75 REMARK 465 GLY I 76 REMARK 465 ASP I 77 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 C 216 O HOH C 222 1.83 REMARK 500 OD1 ASP D 52 O HOH D 101 1.84 REMARK 500 O HOH J 207 O HOH J 218 1.87 REMARK 500 O HOH L 219 O HOH L 221 1.90 REMARK 500 O ASP J 52 O HOH J 201 1.94 REMARK 500 OE2 GLU L 123 O HOH L 201 1.94 REMARK 500 O HOH C 204 O HOH C 207 1.94 REMARK 500 O HOH A 210 O HOH C 210 1.95 REMARK 500 O LEU C 73 O HOH C 201 1.95 REMARK 500 O LEU H 71 O HOH H 101 1.97 REMARK 500 NE2 GLN K 49 O HOH K 101 1.97 REMARK 500 OE2 GLU C 34 O HOH C 202 1.98 REMARK 500 O HOH H 120 O HOH H 121 1.98 REMARK 500 O HOH B 129 O HOH B 131 1.99 REMARK 500 O TYR E 59 O HOH E 101 2.02 REMARK 500 O GLY K 47 O HOH K 102 2.02 REMARK 500 OG SER K 65 O HOH K 103 2.02 REMARK 500 OE1 GLU A 138 O HOH A 201 2.02 REMARK 500 OE1 GLU F 115 O HOH F 201 2.03 REMARK 500 NH2 ARG G 166 O HOH G 201 2.03 REMARK 500 NH1 ARG F 165 O HOH F 202 2.04 REMARK 500 OG1 THR I 66 O HOH I 101 2.10 REMARK 500 O GLU G 191 O HOH G 202 2.11 REMARK 500 NE2 GLN B 49 O HOH B 101 2.11 REMARK 500 NH1 ARG G 117 O HOH G 203 2.12 REMARK 500 O HOH B 109 O HOH B 128 2.14 REMARK 500 OE2 GLU A 162 NH2 ARG A 165 2.14 REMARK 500 ND1 HIS D 68 O HOH D 102 2.15 REMARK 500 OE1 GLN B 40 O HOH B 102 2.15 REMARK 500 OE1 GLU A 162 NH1 ARG A 166 2.15 REMARK 500 OG SER L 183 O HOH L 202 2.16 REMARK 500 NH2 ARG B 54 O HOH B 103 2.16 REMARK 500 O HOH D 112 O HOH E 110 2.16 REMARK 500 OE1 GLU A 169 O HOH A 202 2.16 REMARK 500 NZ LYS C 27 O HOH C 203 2.16 REMARK 500 O HOH A 226 O HOH A 233 2.16 REMARK 500 NZ LYS D 63 O GLY E 76 2.17 REMARK 500 OE2 GLU A 135 O HOH A 203 2.19 REMARK 500 O HOH G 206 O HOH G 220 2.19 REMARK 500 OE2 GLU H 24 O HOH H 102 2.19 REMARK 500 OE2 GLU C 18 O HOH C 204 2.19 REMARK 500 OE1 GLU I 16 O HOH I 102 2.19 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 CB CYS G 190 SG CYS F 190 1554 2.11 REMARK 500 SG CYS A 190 CB CYS L 190 1556 2.14 REMARK 500 NH2 ARG A 166 OD2 ASP B 32 2456 2.18 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 PRO G 113 30.81 -81.07 REMARK 500 GLN E 62 -165.29 -106.48 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 GLY H 75 GLY H 76 -146.28 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 F 224 DISTANCE = 5.81 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL J 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide CYS G 190 and CYS F REMARK 800 190 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide LYS I 63 and GLY H REMARK 800 76 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide LYS J 63 and GLY K REMARK 800 76 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5XIS RELATED DB: PDB REMARK 900 RELATED ID: 5XIT RELATED DB: PDB REMARK 900 RELATED ID: 5XIU RELATED DB: PDB DBREF 5YDK A 113 194 UNP Q8IYW5 RN168_HUMAN 113 194 DBREF 5YDK B 1 76 UNP P62979 RS27A_HUMAN 1 76 DBREF 5YDK D 1 77 UNP P62979 RS27A_HUMAN 1 77 DBREF 5YDK G 113 194 UNP Q8IYW5 RN168_HUMAN 113 194 DBREF 5YDK H 1 76 UNP P62979 RS27A_HUMAN 1 76 DBREF 5YDK J 1 77 UNP P62979 RS27A_HUMAN 1 77 DBREF 5YDK F 113 194 UNP Q8IYW5 RN168_HUMAN 113 194 DBREF 5YDK E 1 76 UNP P62979 RS27A_HUMAN 1 76 DBREF 5YDK C 1 77 UNP P62979 RS27A_HUMAN 1 77 DBREF 5YDK L 113 194 UNP Q8IYW5 RN168_HUMAN 113 194 DBREF 5YDK K 1 76 UNP P62979 RS27A_HUMAN 1 76 DBREF 5YDK I 1 77 UNP P62979 RS27A_HUMAN 1 77 SEQADV 5YDK GLY A 108 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK PRO A 109 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK GLY A 110 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK HIS A 111 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK MET A 112 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK ARG B 63 UNP P62979 LYS 63 ENGINEERED MUTATION SEQADV 5YDK ASP D 77 UNP P62979 ALA 77 CONFLICT SEQADV 5YDK GLY G 108 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK PRO G 109 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK GLY G 110 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK HIS G 111 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK MET G 112 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK ARG H 63 UNP P62979 LYS 63 ENGINEERED MUTATION SEQADV 5YDK ASP J 77 UNP P62979 ALA 77 CONFLICT SEQADV 5YDK GLY F 108 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK PRO F 109 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK GLY F 110 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK HIS F 111 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK MET F 112 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK ARG E 63 UNP P62979 LYS 63 ENGINEERED MUTATION SEQADV 5YDK ASP C 77 UNP P62979 ALA 77 CONFLICT SEQADV 5YDK GLY L 108 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK PRO L 109 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK GLY L 110 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK HIS L 111 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK MET L 112 UNP Q8IYW5 EXPRESSION TAG SEQADV 5YDK ARG K 63 UNP P62979 LYS 63 ENGINEERED MUTATION SEQADV 5YDK ASP I 77 UNP P62979 ALA 77 CONFLICT SEQRES 1 A 87 GLY PRO GLY HIS MET PRO GLY GLU LEU ARG ARG GLU TYR SEQRES 2 A 87 GLU GLU GLU ILE SER LYS VAL ALA ALA GLU ARG ARG ALA SEQRES 3 A 87 SER GLU GLU GLU GLU ASN LYS ALA SER GLU GLU TYR ILE SEQRES 4 A 87 GLN ARG LEU LEU ALA GLU GLU GLU GLU GLU GLU LYS ARG SEQRES 5 A 87 GLN ALA GLU LYS ARG ARG ARG ALA MET GLU GLU GLN LEU SEQRES 6 A 87 LYS SER ASP GLU GLU LEU ALA ARG LYS LEU SER ILE ASP SEQRES 7 A 87 ILE ASN ASN PHE CYS GLU GLY SER ILE SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 D 77 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 D 77 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 D 77 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 D 77 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 D 77 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 D 77 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY ASP SEQRES 1 G 87 GLY PRO GLY HIS MET PRO GLY GLU LEU ARG ARG GLU TYR SEQRES 2 G 87 GLU GLU GLU ILE SER LYS VAL ALA ALA GLU ARG ARG ALA SEQRES 3 G 87 SER GLU GLU GLU GLU ASN LYS ALA SER GLU GLU TYR ILE SEQRES 4 G 87 GLN ARG LEU LEU ALA GLU GLU GLU GLU GLU GLU LYS ARG SEQRES 5 G 87 GLN ALA GLU LYS ARG ARG ARG ALA MET GLU GLU GLN LEU SEQRES 6 G 87 LYS SER ASP GLU GLU LEU ALA ARG LYS LEU SER ILE ASP SEQRES 7 G 87 ILE ASN ASN PHE CYS GLU GLY SER ILE SEQRES 1 H 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 H 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 H 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 H 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 H 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 H 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 J 77 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 J 77 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 J 77 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 J 77 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 J 77 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 J 77 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY ASP SEQRES 1 F 87 GLY PRO GLY HIS MET PRO GLY GLU LEU ARG ARG GLU TYR SEQRES 2 F 87 GLU GLU GLU ILE SER LYS VAL ALA ALA GLU ARG ARG ALA SEQRES 3 F 87 SER GLU GLU GLU GLU ASN LYS ALA SER GLU GLU TYR ILE SEQRES 4 F 87 GLN ARG LEU LEU ALA GLU GLU GLU GLU GLU GLU LYS ARG SEQRES 5 F 87 GLN ALA GLU LYS ARG ARG ARG ALA MET GLU GLU GLN LEU SEQRES 6 F 87 LYS SER ASP GLU GLU LEU ALA ARG LYS LEU SER ILE ASP SEQRES 7 F 87 ILE ASN ASN PHE CYS GLU GLY SER ILE SEQRES 1 E 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 E 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 E 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 E 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 E 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 E 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 C 77 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 77 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 77 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 77 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 77 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 77 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY ASP SEQRES 1 L 87 GLY PRO GLY HIS MET PRO GLY GLU LEU ARG ARG GLU TYR SEQRES 2 L 87 GLU GLU GLU ILE SER LYS VAL ALA ALA GLU ARG ARG ALA SEQRES 3 L 87 SER GLU GLU GLU GLU ASN LYS ALA SER GLU GLU TYR ILE SEQRES 4 L 87 GLN ARG LEU LEU ALA GLU GLU GLU GLU GLU GLU LYS ARG SEQRES 5 L 87 GLN ALA GLU LYS ARG ARG ARG ALA MET GLU GLU GLN LEU SEQRES 6 L 87 LYS SER ASP GLU GLU LEU ALA ARG LYS LEU SER ILE ASP SEQRES 7 L 87 ILE ASN ASN PHE CYS GLU GLY SER ILE SEQRES 1 K 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 K 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 K 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 K 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 K 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 K 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 I 77 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 I 77 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 I 77 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 I 77 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 I 77 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 I 77 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY ASP HET GOL J 101 6 HET GOL C 101 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 13 GOL 2(C3 H8 O3) FORMUL 15 HOH *278(H2 O) HELIX 1 AA1 HIS A 111 LYS A 126 1 16 HELIX 2 AA2 LYS A 126 CYS A 190 1 65 HELIX 3 AA3 THR B 22 GLY B 35 1 14 HELIX 4 AA4 PRO B 37 ASP B 39 5 3 HELIX 5 AA5 THR D 22 GLY D 35 1 14 HELIX 6 AA6 PRO D 37 GLN D 41 5 5 HELIX 7 AA7 PRO G 113 LYS G 126 1 14 HELIX 8 AA8 LYS G 126 GLU G 191 1 66 HELIX 9 AA9 THR H 22 GLY H 35 1 14 HELIX 10 AB1 PRO H 37 ASP H 39 5 3 HELIX 11 AB2 LEU H 56 ASN H 60 5 5 HELIX 12 AB3 THR J 22 GLY J 35 1 14 HELIX 13 AB4 PRO J 37 ASP J 39 5 3 HELIX 14 AB5 ARG F 117 GLU F 191 1 75 HELIX 15 AB6 THR E 22 GLY E 35 1 14 HELIX 16 AB7 PRO E 37 ASP E 39 5 3 HELIX 17 AB8 THR C 22 GLY C 35 1 14 HELIX 18 AB9 PRO C 37 ASP C 39 5 3 HELIX 19 AC1 ARG L 117 CYS L 190 1 74 HELIX 20 AC2 THR K 22 GLY K 35 1 14 HELIX 21 AC3 PRO K 37 ASP K 39 5 3 HELIX 22 AC4 LEU K 56 ASN K 60 5 5 HELIX 23 AC5 THR I 22 GLY I 35 1 14 HELIX 24 AC6 PRO I 37 GLN I 41 5 5 SHEET 1 AA1 5 THR B 12 GLU B 16 0 SHEET 2 AA1 5 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 AA1 5 THR B 66 LEU B 71 1 O LEU B 69 N LYS B 6 SHEET 4 AA1 5 GLN B 41 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA1 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 AA2 5 THR D 12 GLU D 16 0 SHEET 2 AA2 5 GLN D 2 THR D 7 -1 N VAL D 5 O ILE D 13 SHEET 3 AA2 5 THR D 66 VAL D 70 1 O LEU D 67 N PHE D 4 SHEET 4 AA2 5 ARG D 42 PHE D 45 -1 N ARG D 42 O VAL D 70 SHEET 5 AA2 5 LYS D 48 GLN D 49 -1 O LYS D 48 N PHE D 45 SHEET 1 AA3 5 THR H 12 GLU H 16 0 SHEET 2 AA3 5 GLN H 2 LYS H 6 -1 N VAL H 5 O ILE H 13 SHEET 3 AA3 5 THR H 66 LEU H 71 1 O LEU H 67 N PHE H 4 SHEET 4 AA3 5 GLN H 41 PHE H 45 -1 N ILE H 44 O HIS H 68 SHEET 5 AA3 5 LYS H 48 GLN H 49 -1 O LYS H 48 N PHE H 45 SHEET 1 AA4 5 THR J 12 GLU J 16 0 SHEET 2 AA4 5 GLN J 2 THR J 7 -1 N VAL J 5 O ILE J 13 SHEET 3 AA4 5 THR J 66 LEU J 71 1 O LEU J 67 N PHE J 4 SHEET 4 AA4 5 GLN J 41 PHE J 45 -1 N ARG J 42 O VAL J 70 SHEET 5 AA4 5 LYS J 48 GLN J 49 -1 O LYS J 48 N PHE J 45 SHEET 1 AA5 4 THR E 12 GLU E 16 0 SHEET 2 AA5 4 GLN E 2 THR E 7 -1 N VAL E 5 O ILE E 13 SHEET 3 AA5 4 THR E 66 LEU E 71 1 O LEU E 67 N LYS E 6 SHEET 4 AA5 4 GLN E 41 ILE E 44 -1 N ARG E 42 O VAL E 70 SHEET 1 AA6 5 THR C 12 GLU C 16 0 SHEET 2 AA6 5 GLN C 2 THR C 7 -1 N VAL C 5 O ILE C 13 SHEET 3 AA6 5 THR C 66 LEU C 71 1 O LEU C 67 N LYS C 6 SHEET 4 AA6 5 GLN C 41 PHE C 45 -1 N ARG C 42 O VAL C 70 SHEET 5 AA6 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 SHEET 1 AA7 5 THR K 12 GLU K 16 0 SHEET 2 AA7 5 GLN K 2 THR K 7 -1 N VAL K 5 O ILE K 13 SHEET 3 AA7 5 THR K 66 LEU K 71 1 O LEU K 67 N LYS K 6 SHEET 4 AA7 5 GLN K 41 PHE K 45 -1 N ARG K 42 O VAL K 70 SHEET 5 AA7 5 LYS K 48 GLN K 49 -1 O LYS K 48 N PHE K 45 SHEET 1 AA8 5 THR I 12 GLU I 16 0 SHEET 2 AA8 5 GLN I 2 THR I 7 -1 N VAL I 5 O ILE I 13 SHEET 3 AA8 5 THR I 66 VAL I 70 1 O LEU I 67 N LYS I 6 SHEET 4 AA8 5 ARG I 42 PHE I 45 -1 N ARG I 42 O VAL I 70 SHEET 5 AA8 5 LYS I 48 GLN I 49 -1 O LYS I 48 N PHE I 45 SSBOND 1 CYS A 190 CYS L 190 1555 1556 2.01 SSBOND 2 CYS G 190 CYS F 190 1555 1554 2.02 LINK CB CYS A 190 SG CYS L 190 1555 1556 1.66 LINK C GLY B 76 NZ LYS C 63 1555 1555 1.33 LINK NZ LYS D 63 C GLY E 76 1555 1555 1.31 LINK SG CYS G 190 CB CYS F 190 1555 1554 1.55 LINK C GLY H 76 NZ LYS I 63 1555 1555 1.34 LINK NZ LYS J 63 C GLY K 76 1555 1555 1.33 SITE 1 AC1 7 MET J 1 GLU J 16 GLU J 18 HOH J 208 SITE 2 AC1 7 TYR L 145 ARG L 148 GLU L 152 SITE 1 AC2 7 TYR A 145 ARG A 148 GLU A 152 MET C 1 SITE 2 AC2 7 GLU C 16 HOH C 207 HOH C 210 SITE 1 AC3 12 ARG C 72 ILE F 186 ASN F 187 ASN F 188 SITE 2 AC3 12 PHE F 189 GLU F 191 ILE G 186 ASN G 187 SITE 3 AC3 12 ASN G 188 PHE G 189 GLU G 191 ARG J 72 SITE 1 AC4 15 GLU G 153 MET H 1 GLN H 62 GLU H 64 SITE 2 AC4 15 SER H 65 LEU H 73 GLY H 75 HOH H 107 SITE 3 AC4 15 MET I 1 GLN I 2 GLN I 62 GLU I 64 SITE 4 AC4 15 SER I 65 HOH I 116 HOH I 119 SITE 1 AC5 12 GLN J 2 GLN J 62 GLU J 64 SER J 65 SITE 2 AC5 12 HOH J 214 MET K 1 GLN K 62 GLU K 64 SITE 3 AC5 12 SER K 65 LEU K 73 ARG K 74 GLY K 75 CRYST1 85.344 64.120 117.464 90.00 109.62 90.00 P 1 21 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 0.011717 0.000000 0.004178 0.00000 SCALE2 0.000000 0.015596 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009038 0.00000