PDB Short entry for 5TDD HEADER LIGASE 19-SEP-16 5TDD TITLE HUMAN UBR-BOX FROM UBR2 IN COMPLEX WITH HIFS PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE UBR2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: N-RECOGNIN-2,UBIQUITIN-PROTEIN LIGASE E3-ALPHA-2,UBIQUITIN- COMPND 5 PROTEIN LIGASE E3-ALPHA-II; COMPND 6 EC: 6.3.2.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HIS-ILE-PHE-SER PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 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: UBR2, C6ORF133, KIAA0349; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS UBR-BOX, N-END RULE, ZINC FINGER, N-DEGRON, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.MUNOZ-ESCOBAR,G.KOZLOV,K.GEHRING REVDAT 6 04-OCT-23 5TDD 1 LINK REVDAT 5 08-JAN-20 5TDD 1 REMARK REVDAT 4 20-SEP-17 5TDD 1 REMARK REVDAT 3 10-MAY-17 5TDD 1 JRNL REVDAT 2 26-APR-17 5TDD 1 JRNL REVDAT 1 22-MAR-17 5TDD 0 JRNL AUTH J.MUNOZ-ESCOBAR,E.MATTA-CAMACHO,C.CHO,G.KOZLOV,K.GEHRING JRNL TITL BOUND WATERS MEDIATE BINDING OF DIVERSE SUBSTRATES TO A JRNL TITL 2 UBIQUITIN LIGASE. JRNL REF STRUCTURE V. 25 719 2017 JRNL REFN ISSN 1878-4186 JRNL PMID 28392261 JRNL DOI 10.1016/J.STR.2017.03.004 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9083 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.111 REMARK 3 R VALUE (WORKING SET) : 0.106 REMARK 3 FREE R VALUE : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.050 REMARK 3 FREE R VALUE TEST SET COUNT : 913 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 20.7293 - 2.9634 1.00 1170 135 0.1296 0.1574 REMARK 3 2 2.9634 - 2.3532 1.00 1174 135 0.1146 0.1616 REMARK 3 3 2.3532 - 2.0560 1.00 1165 121 0.0857 0.1309 REMARK 3 4 2.0560 - 1.8682 1.00 1181 128 0.0850 0.1356 REMARK 3 5 1.8682 - 1.7343 1.00 1149 129 0.0831 0.1587 REMARK 3 6 1.7343 - 1.6321 1.00 1158 131 0.0835 0.1395 REMARK 3 7 1.6321 - 1.5504 1.00 1173 134 0.0915 0.1865 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.010 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 : 0.010 616 REMARK 3 ANGLE : 0.963 824 REMARK 3 CHIRALITY : 0.063 81 REMARK 3 PLANARITY : 0.008 109 REMARK 3 DIHEDRAL : 11.688 357 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 5TDD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000223363. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.6362 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9083 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 20.727 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.55800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3NY3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.5, 12% PEG 20000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 37.07550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.53775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.61325 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: 700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 93 REMARK 465 PRO A 94 REMARK 465 LEU A 95 REMARK 465 LEU A 168 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 SER B 4 OG 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 A 342 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A 343 DISTANCE = 7.18 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 99 SG REMARK 620 2 CYS A 124 SG 120.5 REMARK 620 3 CYS A 127 SG 107.4 93.7 REMARK 620 4 CYS A 149 SG 106.7 115.0 112.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 112 SG REMARK 620 2 CYS A 115 SG 114.6 REMARK 620 3 HIS A 133 ND1 110.9 103.9 REMARK 620 4 HIS A 136 ND1 112.9 105.0 109.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 127 SG REMARK 620 2 CYS A 151 SG 109.8 REMARK 620 3 CYS A 163 SG 109.8 111.1 REMARK 620 4 HIS A 166 ND1 102.9 117.1 105.7 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TDA RELATED DB: PDB REMARK 900 RELATED ID: 5TDB RELATED DB: PDB REMARK 900 RELATED ID: 5TDC RELATED DB: PDB DBREF 5TDD A 98 168 UNP Q8IWV8 UBR2_HUMAN 98 168 DBREF 5TDD B 1 4 PDB 5TDD 5TDD 1 4 SEQADV 5TDD GLY A 93 UNP Q8IWV8 EXPRESSION TAG SEQADV 5TDD PRO A 94 UNP Q8IWV8 EXPRESSION TAG SEQADV 5TDD LEU A 95 UNP Q8IWV8 EXPRESSION TAG SEQADV 5TDD GLY A 96 UNP Q8IWV8 EXPRESSION TAG SEQADV 5TDD SER A 97 UNP Q8IWV8 EXPRESSION TAG SEQRES 1 A 76 GLY PRO LEU GLY SER LEU CYS GLY ARG VAL PHE LYS VAL SEQRES 2 A 76 GLY GLU PRO THR TYR SER CYS ARG ASP CYS ALA VAL ASP SEQRES 3 A 76 PRO THR CYS VAL LEU CYS MET GLU CYS PHE LEU GLY SER SEQRES 4 A 76 ILE HIS ARG ASP HIS ARG TYR ARG MET THR THR SER GLY SEQRES 5 A 76 GLY GLY GLY PHE CYS ASP CYS GLY ASP THR GLU ALA TRP SEQRES 6 A 76 LYS GLU GLY PRO TYR CYS GLN LYS HIS GLU LEU SEQRES 1 B 4 HIS ILE PHE SER HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HET EDO A 204 10 HET EDO A 205 10 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 3(ZN 2+) FORMUL 6 EDO 2(C2 H6 O2) FORMUL 8 HOH *44(H2 O) HELIX 1 AA1 MET A 125 GLY A 130 1 6 HELIX 2 AA2 SER A 131 HIS A 136 5 6 SHEET 1 AA1 3 LEU A 123 CYS A 124 0 SHEET 2 AA1 3 PRO A 108 CYS A 112 -1 N TYR A 110 O LEU A 123 SHEET 3 AA1 3 TYR A 138 THR A 142 -1 O ARG A 139 N SER A 111 LINK SG CYS A 99 ZN ZN A 201 1555 1555 2.32 LINK SG CYS A 112 ZN ZN A 203 1555 1555 2.29 LINK SG CYS A 115 ZN ZN A 203 1555 1555 2.31 LINK SG CYS A 124 ZN ZN A 201 1555 1555 2.35 LINK SG CYS A 127 ZN ZN A 201 1555 1555 2.39 LINK SG CYS A 127 ZN ZN A 202 1555 1555 2.37 LINK ND1 HIS A 133 ZN ZN A 203 1555 1555 2.06 LINK ND1 HIS A 136 ZN ZN A 203 1555 1555 2.06 LINK SG CYS A 149 ZN ZN A 201 1555 1555 2.35 LINK SG CYS A 151 ZN ZN A 202 1555 1555 2.31 LINK SG CYS A 163 ZN ZN A 202 1555 1555 2.31 LINK ND1 HIS A 166 ZN ZN A 202 1555 1555 2.06 SITE 1 AC1 4 CYS A 99 CYS A 124 CYS A 127 CYS A 149 SITE 1 AC2 4 CYS A 127 CYS A 151 CYS A 163 HIS A 166 SITE 1 AC3 4 CYS A 112 CYS A 115 HIS A 133 HIS A 136 SITE 1 AC4 4 GLY A 100 LEU A 129 ARG A 134 PHE A 148 SITE 1 AC5 4 HIS A 136 TYR A 138 ASP A 153 HOH A 328 CRYST1 29.313 29.313 74.151 90.00 90.00 90.00 P 41 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.034115 0.000000 0.000000 0.00000 SCALE2 0.000000 0.034115 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013486 0.00000