HEADER DNA BINDING PROTEIN 05-MAR-20 6W2G TITLE CRYSTAL STRUCTURE OF Y188G VARIANT OF THE INTERNAL UBA DOMAIN OF TITLE 2 HHR23A IN MONOCLINIC UNIT CELL COMPND MOL_ID: 1; COMPND 2 MOLECULE: UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HHR23A; COMPND 5 ENGINEERED: YES; COMPND 6 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: RAD23A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS UBIQUITIN ASSOCIATED DOMAIN, UBA DOMAIN, DNA BINDING PROTEIN, HELICAL KEYWDS 2 BUNDLE EXPDTA X-RAY DIFFRACTION AUTHOR B.E.BOWLER,B.ZENG,D.C.BECHT,M.ROTHFUSS,S.R.SPRANG,T.-C.MOU REVDAT 4 03-APR-24 6W2G 1 REMARK REVDAT 3 01-NOV-23 6W2G 1 JRNL REVDAT 2 25-AUG-21 6W2G 1 REMARK DBREF SEQADV HELIX REVDAT 2 2 1 SITE ATOM REVDAT 1 10-MAR-21 6W2G 0 JRNL AUTH M.T.ROTHFUSS,D.C.BECHT,B.ZENG,L.J.MCCLELLAND,C.YATES-HANSEN, JRNL AUTH 2 B.E.BOWLER JRNL TITL HIGH-ACCURACY PREDICTION OF STABILIZING SURFACE MUTATIONS TO JRNL TITL 2 THE THREE-HELIX BUNDLE, UBA(1), WITH EMCAST. JRNL REF J.AM.CHEM.SOC. V. 145 22979 2023 JRNL REFN ESSN 1520-5126 JRNL PMID 37815921 JRNL DOI 10.1021/JACS.3C04966 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1-3660 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.450 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 29568 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1763 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 32.8800 - 2.5900 0.99 2290 145 0.1560 0.1719 REMARK 3 2 2.5900 - 2.0500 0.98 2237 142 0.1372 0.1408 REMARK 3 3 2.0500 - 1.7900 0.99 2256 143 0.1319 0.1415 REMARK 3 4 1.7900 - 1.6300 0.97 2186 140 0.1259 0.1294 REMARK 3 5 1.6300 - 1.5100 0.99 2230 147 0.1225 0.1470 REMARK 3 6 1.5100 - 1.4200 0.97 2164 141 0.1244 0.1476 REMARK 3 7 1.4200 - 1.3500 0.96 2184 135 0.1342 0.1597 REMARK 3 8 1.3500 - 1.2900 0.97 2178 138 0.1331 0.1504 REMARK 3 9 1.2900 - 1.2400 0.93 2094 125 0.1363 0.1546 REMARK 3 10 1.2400 - 1.2000 0.93 2110 129 0.1400 0.1463 REMARK 3 11 1.2000 - 1.1600 0.93 2094 140 0.1399 0.1513 REMARK 3 12 1.1600 - 1.1300 0.90 1997 125 0.1499 0.1842 REMARK 3 13 1.1300 - 1.1000 0.80 1785 113 0.1592 0.1695 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.798 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.33 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 : 0.008 771 REMARK 3 ANGLE : 1.036 1039 REMARK 3 CHIRALITY : 0.077 119 REMARK 3 PLANARITY : 0.007 135 REMARK 3 DIHEDRAL : 17.472 116 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 6W2G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247106. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-20 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 : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS MAR 15,2019 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29568 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 33.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.01716 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 56.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.07858 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 16.63 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.17.1-3660 REMARK 200 STARTING MODEL: P43 UBA-1 Y188G STRUCTURE SOLVED BY SULFUR SAD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M PHOSPHATE REMARK 280 -CITRATE PH 4.2, 40%(V/V) ETHYLENE GLYCOL, VAPOR DIFFUSION, REMARK 280 SITTING 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 20.04000 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 154 REMARK 465 SER A 155 REMARK 465 GLY B 154 REMARK 465 SER B 155 REMARK 465 THR B 156 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 176 CD OE1 OE2 REMARK 480 GLU A 178 CG CD OE1 OE2 REMARK 480 GLU B 176 CD OE1 OE2 REMARK 480 GLU B 178 CD REMARK 480 ARG B 179 NE CZ NH1 NH2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 302 DBREF 6W2G A 155 204 UNP P54725 RD23A_HUMAN 155 204 DBREF 6W2G B 155 204 UNP P54725 RD23A_HUMAN 155 204 SEQADV 6W2G GLY A 154 UNP P54725 EXPRESSION TAG SEQADV 6W2G GLY A 188 UNP P54725 TYR 188 ENGINEERED MUTATION SEQADV 6W2G GLY B 154 UNP P54725 EXPRESSION TAG SEQADV 6W2G GLY B 188 UNP P54725 TYR 188 ENGINEERED MUTATION SEQRES 1 A 51 GLY SER THR LEU VAL THR GLY SER GLU TYR GLU THR MET SEQRES 2 A 51 LEU THR GLU ILE MET SER MET GLY TYR GLU ARG GLU ARG SEQRES 3 A 51 VAL VAL ALA ALA LEU ARG ALA SER GLY ASN ASN PRO HIS SEQRES 4 A 51 ARG ALA VAL GLU TYR LEU LEU THR GLY ILE PRO GLY SEQRES 1 B 51 GLY SER THR LEU VAL THR GLY SER GLU TYR GLU THR MET SEQRES 2 B 51 LEU THR GLU ILE MET SER MET GLY TYR GLU ARG GLU ARG SEQRES 3 B 51 VAL VAL ALA ALA LEU ARG ALA SER GLY ASN ASN PRO HIS SEQRES 4 B 51 ARG ALA VAL GLU TYR LEU LEU THR GLY ILE PRO GLY HET EDO A 301 10 HET EDO B 301 10 HET EDO B 302 10 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 3(C2 H6 O2) FORMUL 6 HOH *75(H2 O) HELIX 1 AA1 THR A 159 SER A 172 1 14 HELIX 2 AA2 GLU A 176 SER A 187 1 12 HELIX 3 AA3 ASN A 190 GLY A 201 1 12 HELIX 4 AA4 THR B 159 SER B 172 1 14 HELIX 5 AA5 GLU B 176 SER B 187 1 12 HELIX 6 AA6 ASN B 190 GLY B 201 1 12 SITE 1 AC1 6 GLU A 196 THR A 200 GLY A 201 HOH A 426 SITE 2 AC1 6 PRO B 191 HIS B 192 SITE 1 AC2 5 MET B 173 GLY B 174 TYR B 175 HOH B 415 SITE 2 AC2 5 HOH B 425 SITE 1 AC3 4 THR A 168 ARG B 185 HOH B 404 HOH B 409 CRYST1 29.490 40.080 32.893 90.00 91.39 90.00 P 1 21 1 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 0.033910 0.000000 0.000822 0.00000 SCALE2 0.000000 0.024950 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030411 0.00000 CONECT 1430 1431 1432 1434 1435 CONECT 1431 1430 1436 CONECT 1432 1430 1433 1437 1438 CONECT 1433 1432 1439 CONECT 1434 1430 CONECT 1435 1430 CONECT 1436 1431 CONECT 1437 1432 CONECT 1438 1432 CONECT 1439 1433 CONECT 1440 1441 1442 1444 1445 CONECT 1441 1440 1446 CONECT 1442 1440 1443 1447 1448 CONECT 1443 1442 1449 CONECT 1444 1440 CONECT 1445 1440 CONECT 1446 1441 CONECT 1447 1442 CONECT 1448 1442 CONECT 1449 1443 CONECT 1450 1451 1452 1454 1455 CONECT 1451 1450 1456 CONECT 1452 1450 1453 1457 1458 CONECT 1453 1452 1459 CONECT 1454 1450 CONECT 1455 1450 CONECT 1456 1451 CONECT 1457 1452 CONECT 1458 1452 CONECT 1459 1453 MASTER 240 0 3 6 0 0 5 6 832 2 30 8 END