HEADER APOPTOSIS 07-NOV-12 4HWD TITLE CRYSTAL STRUCTURE OF ATBAG2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 2; COMPND 3 CHAIN: D, A, B; COMPND 4 FRAGMENT: BAG DOMAIN (UNP RESIDUES 129-214); COMPND 5 SYNONYM: BCL-2-ASSOCIATED ATHANOGENE 2; 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: AT5G62100, BAG2, MTG10.13; 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 4HWD 1 SEQADV REVDAT 2 19-JUN-13 4HWD 1 JRNL REVDAT 1 29-MAY-13 4HWD 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. 2.31 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 12931 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 636 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 35.7151 - 3.9521 0.99 2632 136 0.2016 0.2072 REMARK 3 2 3.9521 - 3.1375 1.00 2503 111 0.2299 0.2414 REMARK 3 3 3.1375 - 2.7411 0.99 2415 132 0.2487 0.2600 REMARK 3 4 2.7411 - 2.4905 0.99 2423 135 0.2522 0.2970 REMARK 3 5 2.4905 - 2.3120 0.96 2322 122 0.2457 0.3148 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.61 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 30.30 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.820 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) : 2.82230 REMARK 3 B22 (A**2) : -7.45840 REMARK 3 B33 (A**2) : 4.63610 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 : 0.006 2032 REMARK 3 ANGLE : 0.984 2700 REMARK 3 CHIRALITY : 0.080 314 REMARK 3 PLANARITY : 0.003 342 REMARK 3 DIHEDRAL : 16.070 808 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): -11.6405 -2.0873 23.6578 REMARK 3 T TENSOR REMARK 3 T11: 0.0196 T22: 0.0223 REMARK 3 T33: 0.0207 T12: -0.0163 REMARK 3 T13: -0.0066 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 0.0207 L22: 0.0548 REMARK 3 L33: 0.0565 L12: 0.0079 REMARK 3 L13: -0.0245 L23: -0.0480 REMARK 3 S TENSOR REMARK 3 S11: -0.0091 S12: 0.0311 S13: -0.0136 REMARK 3 S21: 0.0138 S22: 0.0180 S23: -0.0260 REMARK 3 S31: -0.0079 S32: -0.0342 S33: 0.0134 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 4HWD 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_1000076002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-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 : 12982 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.312 REMARK 200 RESOLUTION RANGE LOW (A) : 35.711 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 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) : 2.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 20% PEG3350, REMARK 280 PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 13.06800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.51700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.22600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 88.51700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.06800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.22600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 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: 3 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 133 REMARK 465 PRO A 134 REMARK 465 GLY A 135 REMARK 465 SER A 222 REMARK 465 GLY B 133 REMARK 465 PRO B 134 REMARK 465 GLY B 135 REMARK 465 GLY B 192 REMARK 465 ASP B 193 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 ASP D 193 CG OD1 OD2 REMARK 470 SER B 191 OG REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HWC RELATED DB: PDB REMARK 900 RELATED ID: 4HWF RELATED DB: PDB REMARK 900 RELATED ID: 4HWH RELATED DB: PDB REMARK 900 RELATED ID: 4HWI RELATED DB: PDB DBREF 4HWD D 137 222 UNP Q0WPX7 BAG2_ARATH 129 214 DBREF 4HWD A 137 222 UNP Q0WPX7 BAG2_ARATH 129 214 DBREF 4HWD B 137 222 UNP Q0WPX7 BAG2_ARATH 129 214 SEQADV 4HWD GLY D 133 UNP Q0WPX7 EXPRESSION TAG SEQADV 4HWD PRO D 134 UNP Q0WPX7 EXPRESSION TAG SEQADV 4HWD GLY D 135 UNP Q0WPX7 EXPRESSION TAG SEQADV 4HWD SER D 136 UNP Q0WPX7 EXPRESSION TAG SEQADV 4HWD GLY A 133 UNP Q0WPX7 EXPRESSION TAG SEQADV 4HWD PRO A 134 UNP Q0WPX7 EXPRESSION TAG SEQADV 4HWD GLY A 135 UNP Q0WPX7 EXPRESSION TAG SEQADV 4HWD SER A 136 UNP Q0WPX7 EXPRESSION TAG SEQADV 4HWD GLY B 133 UNP Q0WPX7 EXPRESSION TAG SEQADV 4HWD PRO B 134 UNP Q0WPX7 EXPRESSION TAG SEQADV 4HWD GLY B 135 UNP Q0WPX7 EXPRESSION TAG SEQADV 4HWD SER B 136 UNP Q0WPX7 EXPRESSION TAG SEQRES 1 D 90 GLY PRO GLY SER SER SER LYS ALA ILE SER ASP ILE SER SEQRES 2 D 90 PHE GLN VAL GLU ARG LEU ALA GLY GLN LEU SER ALA PHE SEQRES 3 D 90 ASP THR VAL ILE GLY LYS GLY GLY LYS VAL GLU GLU LYS SEQRES 4 D 90 ASN LEU GLU ASN LEU MET GLU MET LEU MET ASN GLN LEU SEQRES 5 D 90 VAL LYS LEU ASP ALA ILE SER GLY ASP GLY ASP VAL LYS SEQRES 6 D 90 LEU LYS LYS LYS MET GLN GLU GLU ARG LEU HIS LYS TYR SEQRES 7 D 90 VAL GLU ALA LEU ASP LEU LEU LYS ILE LYS ASN SER SEQRES 1 A 90 GLY PRO GLY SER SER SER LYS ALA ILE SER ASP ILE SER SEQRES 2 A 90 PHE GLN VAL GLU ARG LEU ALA GLY GLN LEU SER ALA PHE SEQRES 3 A 90 ASP THR VAL ILE GLY LYS GLY GLY LYS VAL GLU GLU LYS SEQRES 4 A 90 ASN LEU GLU ASN LEU MET GLU MET LEU MET ASN GLN LEU SEQRES 5 A 90 VAL LYS LEU ASP ALA ILE SER GLY ASP GLY ASP VAL LYS SEQRES 6 A 90 LEU LYS LYS LYS MET GLN GLU GLU ARG LEU HIS LYS TYR SEQRES 7 A 90 VAL GLU ALA LEU ASP LEU LEU LYS ILE LYS ASN SER SEQRES 1 B 90 GLY PRO GLY SER SER SER LYS ALA ILE SER ASP ILE SER SEQRES 2 B 90 PHE GLN VAL GLU ARG LEU ALA GLY GLN LEU SER ALA PHE SEQRES 3 B 90 ASP THR VAL ILE GLY LYS GLY GLY LYS VAL GLU GLU LYS SEQRES 4 B 90 ASN LEU GLU ASN LEU MET GLU MET LEU MET ASN GLN LEU SEQRES 5 B 90 VAL LYS LEU ASP ALA ILE SER GLY ASP GLY ASP VAL LYS SEQRES 6 B 90 LEU LYS LYS LYS MET GLN GLU GLU ARG LEU HIS LYS TYR SEQRES 7 B 90 VAL GLU ALA LEU ASP LEU LEU LYS ILE LYS ASN SER FORMUL 4 HOH *182(H2 O) HELIX 1 1 GLY D 133 LYS D 164 1 32 HELIX 2 2 GLU D 169 ILE D 190 1 22 HELIX 3 3 GLY D 194 SER D 222 1 29 HELIX 4 4 SER A 137 LYS A 164 1 28 HELIX 5 5 GLU A 169 ALA A 189 1 21 HELIX 6 6 ASP A 193 ASN A 221 1 29 HELIX 7 7 SER B 137 LYS B 164 1 28 HELIX 8 8 GLU B 169 ALA B 189 1 21 HELIX 9 9 ASP B 195 SER B 222 1 28 CRYST1 26.136 60.452 177.034 90.00 90.00 90.00 P 21 21 21 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 0.038261 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016542 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005649 0.00000