HEADER LIGASE 26-JAN-17 5UM3 TITLE CRYSTAL STRUCTURE OF THE V122L MUTANT OF HUMAN UBR-BOX DOMAIN FROM TITLE 2 UBR2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE UBR2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: N-RECOGNIN-2,RING-TYPE E3 UBIQUITIN TRANSFERASE UBR2, COMPND 5 UBIQUITIN-PROTEIN LIGASE E3-ALPHA-2,UBIQUITIN-PROTEIN LIGASE E3- COMPND 6 ALPHA-II; COMPND 7 EC: 2.3.2.27; COMPND 8 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: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS UBR-BOX DOMAIN, JOHANSSON BLIZARD, ZINC FINGER, N-END RULE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.MUNOZ ESCOBAR,G.KOZLOV,K.GEHRING REVDAT 6 04-OCT-23 5UM3 1 REMARK REVDAT 5 08-JAN-20 5UM3 1 SEQADV REVDAT 4 20-SEP-17 5UM3 1 REMARK REVDAT 3 10-MAY-17 5UM3 1 JRNL REVDAT 2 26-APR-17 5UM3 1 JRNL REVDAT 1 22-MAR-17 5UM3 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. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 18153 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.137 REMARK 3 FREE R VALUE : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1816 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 17.6198 - 2.8145 0.99 1375 155 0.1545 0.1693 REMARK 3 2 2.8145 - 2.2354 1.00 1313 142 0.1406 0.1384 REMARK 3 3 2.2354 - 1.9533 1.00 1287 140 0.1159 0.1443 REMARK 3 4 1.9533 - 1.7748 1.00 1292 148 0.1170 0.1466 REMARK 3 5 1.7748 - 1.6477 1.00 1271 139 0.1063 0.1243 REMARK 3 6 1.6477 - 1.5506 1.00 1269 140 0.1010 0.1347 REMARK 3 7 1.5506 - 1.4730 1.00 1249 143 0.1062 0.1464 REMARK 3 8 1.4730 - 1.4089 1.00 1280 143 0.1216 0.1642 REMARK 3 9 1.4089 - 1.3547 1.00 1264 142 0.1306 0.1553 REMARK 3 10 1.3547 - 1.3080 1.00 1249 136 0.1549 0.2406 REMARK 3 11 1.3080 - 1.2671 0.99 1230 140 0.1726 0.2074 REMARK 3 12 1.2671 - 1.2309 0.94 1195 132 0.2040 0.2134 REMARK 3 13 1.2309 - 1.1985 0.84 1063 116 0.2377 0.2917 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.430 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 : 0.006 590 REMARK 3 ANGLE : 0.953 798 REMARK 3 CHIRALITY : 0.070 78 REMARK 3 PLANARITY : 0.006 109 REMARK 3 DIHEDRAL : 12.220 221 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 5UM3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000226109. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-16 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 : 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) : 0.6263 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18167 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.198 REMARK 200 RESOLUTION RANGE LOW (A) : 17.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.09856 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.54600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.610 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: 5TDD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5 25% PEG 4000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 14.58850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.02600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.68750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.02600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.58850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 14.68750 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 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 ARG A 137 CD NE CZ NH1 NH2 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 HE ARG A 113 O HOH A 301 1.52 REMARK 500 O HOH A 340 O HOH A 345 1.91 REMARK 500 O HOH A 385 O HOH A 386 2.04 REMARK 500 O HOH A 302 O HOH A 370 2.10 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 A 392 DISTANCE = 6.31 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 120.2 REMARK 620 3 CYS A 127 SG 105.8 93.5 REMARK 620 4 CYS A 149 SG 109.9 113.3 112.6 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 116.1 REMARK 620 3 HIS A 133 ND1 110.4 103.4 REMARK 620 4 HIS A 136 ND1 110.3 103.8 112.6 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 110.9 REMARK 620 3 CYS A 163 SG 110.2 110.5 REMARK 620 4 HIS A 166 ND1 100.7 120.6 103.3 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 DBREF 5UM3 A 98 167 UNP Q8IWV8 UBR2_HUMAN 98 167 SEQADV 5UM3 GLY A 93 UNP Q8IWV8 EXPRESSION TAG SEQADV 5UM3 PRO A 94 UNP Q8IWV8 EXPRESSION TAG SEQADV 5UM3 LEU A 95 UNP Q8IWV8 EXPRESSION TAG SEQADV 5UM3 GLY A 96 UNP Q8IWV8 EXPRESSION TAG SEQADV 5UM3 SER A 97 UNP Q8IWV8 EXPRESSION TAG SEQADV 5UM3 LEU A 122 UNP Q8IWV8 VAL 122 ENGINEERED MUTATION SEQRES 1 A 75 GLY PRO LEU GLY SER LEU CYS GLY ARG VAL PHE LYS VAL SEQRES 2 A 75 GLY GLU PRO THR TYR SER CYS ARG ASP CYS ALA VAL ASP SEQRES 3 A 75 PRO THR CYS LEU LEU CYS MET GLU CYS PHE LEU GLY SER SEQRES 4 A 75 ILE HIS ARG ASP HIS ARG TYR ARG MET THR THR SER GLY SEQRES 5 A 75 GLY GLY GLY PHE CYS ASP CYS GLY ASP THR GLU ALA TRP SEQRES 6 A 75 LYS GLU GLY PRO TYR CYS GLN LYS HIS GLU HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HETNAM ZN ZINC ION FORMUL 2 ZN 3(ZN 2+) FORMUL 5 HOH *92(H2 O) HELIX 1 AA1 CYS A 124 GLY A 130 1 7 HELIX 2 AA2 SER A 131 HIS A 136 5 6 SHEET 1 AA1 2 PRO A 108 CYS A 112 0 SHEET 2 AA1 2 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 2.30 LINK SG CYS A 112 ZN ZN A 203 1555 1555 2.29 LINK SG CYS A 115 ZN ZN A 203 1555 1555 2.29 LINK SG CYS A 124 ZN ZN A 201 1555 1555 2.34 LINK SG CYS A 127 ZN ZN A 201 1555 1555 2.39 LINK SG CYS A 127 ZN ZN A 202 1555 1555 2.36 LINK ND1 HIS A 133 ZN ZN A 203 1555 1555 2.07 LINK ND1 HIS A 136 ZN ZN A 203 1555 1555 2.05 LINK SG CYS A 149 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 151 ZN ZN A 202 1555 1555 2.30 LINK SG CYS A 163 ZN ZN A 202 1555 1555 2.32 LINK ND1 HIS A 166 ZN ZN A 202 1555 1555 2.07 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 CRYST1 29.177 29.375 66.052 90.00 90.00 90.00 P 21 21 21 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 0.034274 0.000000 0.000000 0.00000 SCALE2 0.000000 0.034043 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015140 0.00000