HEADER APOPTOSIS 07-NOV-12 4HWF TITLE CRYSTAL STRUCTURE OF ATBAG3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: BAG DOMAIN (UNP RESIDUES 135-220); COMPND 5 SYNONYM: BCL-2-ASSOCIATED ATHANOGENE 3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: AT5G07220, BAG3, T28J14_160; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS THREE HELIX BUNDLE, CO-CHAPERONE, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR Y.SHEN,S.FANG REVDAT 3 28-FEB-24 4HWF 1 REMARK SEQADV REVDAT 2 19-JUN-13 4HWF 1 JRNL REVDAT 1 29-MAY-13 4HWF 0 JRNL AUTH S.FANG,L.LI,B.CUI,S.MEN,Y.SHEN,X.YANG JRNL TITL STRUCTURAL INSIGHT INTO PLANT PROGRAMMED CELL DEATH MEDIATED JRNL TITL 2 BY BAG PROTEINS IN ARABIDOPSIS THALIANA. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 934 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23695238 JRNL DOI 10.1107/S0907444913003624 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.550 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 21455 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1996 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 32.2868 - 4.8159 1.00 1559 161 0.2319 0.2801 REMARK 3 2 4.8159 - 3.8245 1.00 1473 154 0.2019 0.2115 REMARK 3 3 3.8245 - 3.3416 1.00 1444 151 0.2054 0.2231 REMARK 3 4 3.3416 - 3.0363 0.99 1418 149 0.2123 0.2403 REMARK 3 5 3.0363 - 2.8188 0.99 1410 147 0.2301 0.2541 REMARK 3 6 2.8188 - 2.6527 0.99 1379 138 0.2270 0.2581 REMARK 3 7 2.6527 - 2.5199 0.98 1404 146 0.2177 0.2325 REMARK 3 8 2.5199 - 2.4103 0.98 1392 129 0.2170 0.2390 REMARK 3 9 2.4103 - 2.3175 0.98 1356 141 0.2013 0.2421 REMARK 3 10 2.3175 - 2.2376 0.97 1359 139 0.2049 0.2512 REMARK 3 11 2.2376 - 2.1676 0.96 1365 141 0.2094 0.2531 REMARK 3 12 2.1676 - 2.1057 0.95 1325 136 0.2234 0.2387 REMARK 3 13 2.1057 - 2.0502 0.95 1330 138 0.2419 0.2552 REMARK 3 14 2.0502 - 2.0000 0.89 1246 126 0.2811 0.3014 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 38.46 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.920 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) : -1.78280 REMARK 3 B22 (A**2) : -1.78280 REMARK 3 B33 (A**2) : 1.72490 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1271 REMARK 3 ANGLE : 0.841 1701 REMARK 3 CHIRALITY : 0.056 208 REMARK 3 PLANARITY : 0.003 213 REMARK 3 DIHEDRAL : 13.917 493 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 10.4859 17.9531 67.2494 REMARK 3 T TENSOR REMARK 3 T11: 0.0131 T22: 0.1368 REMARK 3 T33: 0.0259 T12: -0.0647 REMARK 3 T13: -0.0182 T23: -0.0569 REMARK 3 L TENSOR REMARK 3 L11: 0.0655 L22: 0.0542 REMARK 3 L33: 0.3062 L12: 0.0544 REMARK 3 L13: 0.1059 L23: 0.0805 REMARK 3 S TENSOR REMARK 3 S11: 0.0160 S12: 0.0193 S13: -0.0316 REMARK 3 S21: 0.0162 S22: 0.0335 S23: -0.0268 REMARK 3 S31: -0.0278 S32: 0.2091 S33: -0.0700 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 4HWF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000076004. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21455 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 32.283 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES SODIUM, 1.7 M LITHIUM REMARK 280 SULFATE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 115.67733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.83867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 57.83867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 115.67733 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 133 REMARK 465 GLY B 133 REMARK 465 GLU B 157 REMARK 465 THR B 158 REMARK 465 VAL B 159 REMARK 465 ILE B 160 REMARK 465 ASN B 161 REMARK 465 LYS B 162 REMARK 465 GLY B 163 REMARK 465 GLY B 164 REMARK 465 LYS B 165 REMARK 465 VAL B 166 REMARK 465 GLU B 167 REMARK 465 SER B 220 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 134 OG REMARK 470 GLU B 168 CG CD OE1 OE2 REMARK 470 LYS B 169 CG CD CE NZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HWC RELATED DB: PDB REMARK 900 RELATED ID: 4HWD RELATED DB: PDB REMARK 900 RELATED ID: 4HWH RELATED DB: PDB REMARK 900 RELATED ID: 4HWI RELATED DB: PDB DBREF 4HWF A 135 220 UNP Q9LYP4 BAG3_ARATH 135 220 DBREF 4HWF B 135 220 UNP Q9LYP4 BAG3_ARATH 135 220 SEQADV 4HWF GLY A 133 UNP Q9LYP4 EXPRESSION TAG SEQADV 4HWF SER A 134 UNP Q9LYP4 EXPRESSION TAG SEQADV 4HWF GLY B 133 UNP Q9LYP4 EXPRESSION TAG SEQADV 4HWF SER B 134 UNP Q9LYP4 EXPRESSION TAG SEQRES 1 A 88 GLY SER ALA SER LYS SER ILE SER ASP ILE SER PHE GLU SEQRES 2 A 88 VAL ASP ARG LEU ALA GLY GLN VAL SER ALA PHE GLU THR SEQRES 3 A 88 VAL ILE ASN LYS GLY GLY LYS VAL GLU GLU LYS SER LEU SEQRES 4 A 88 VAL ASN LEU ILE GLU MET LEU MET ASN GLN LEU LEU ARG SEQRES 5 A 88 LEU ASP ALA ILE ILE ALA ASP GLY ASP VAL LYS LEU MET SEQRES 6 A 88 ARG LYS MET GLN VAL GLN ARG VAL GLN LYS TYR VAL GLU SEQRES 7 A 88 ALA LEU ASP LEU LEU LYS VAL LYS ASN SER SEQRES 1 B 88 GLY SER ALA SER LYS SER ILE SER ASP ILE SER PHE GLU SEQRES 2 B 88 VAL ASP ARG LEU ALA GLY GLN VAL SER ALA PHE GLU THR SEQRES 3 B 88 VAL ILE ASN LYS GLY GLY LYS VAL GLU GLU LYS SER LEU SEQRES 4 B 88 VAL ASN LEU ILE GLU MET LEU MET ASN GLN LEU LEU ARG SEQRES 5 B 88 LEU ASP ALA ILE ILE ALA ASP GLY ASP VAL LYS LEU MET SEQRES 6 B 88 ARG LYS MET GLN VAL GLN ARG VAL GLN LYS TYR VAL GLU SEQRES 7 B 88 ALA LEU ASP LEU LEU LYS VAL LYS ASN SER HET SO4 A 301 5 HET SO4 B 301 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *141(H2 O) HELIX 1 1 SER A 134 LYS A 162 1 29 HELIX 2 2 GLU A 167 ALA A 190 1 24 HELIX 3 3 ASP A 193 ASN A 219 1 27 HELIX 4 4 ALA B 135 ALA B 150 1 16 HELIX 5 5 SER B 170 ASP B 191 1 22 HELIX 6 6 ASP B 193 ASP B 213 1 21 SITE 1 AC1 3 THR A 158 ASN A 161 HOH A 473 SITE 1 AC2 3 LYS A 207 GLY B 151 GLN B 152 CRYST1 55.807 55.807 173.516 90.00 90.00 120.00 P 32 2 1 12 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 0.017919 0.010345 0.000000 0.00000 SCALE2 0.000000 0.020691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005763 0.00000