HEADER DNA BINDING PROTEIN 11-NOV-11 3ULX TITLE CRYSTAL STRUCTURAL OF THE CONSERVED DOMAIN OF RICE STRESS-RESPONSIVE TITLE 2 NAC1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STRESS-INDUCED TRANSCRIPTION FACTOR NAC1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-174; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA SUBSP. JAPONICA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 39947; SOURCE 5 GENE: SNAC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS NAC FAMILY, STRESS-RESPONSIVE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.Y.LOU,Q.F.CHEN,Q.WANG,L.Z.XIONG REVDAT 2 01-NOV-23 3ULX 1 REMARK REVDAT 1 28-DEC-11 3ULX 0 JRNL AUTH Z.Y.LOU,Q.F.CHEN,Q.WANG,L.Z.XIONG JRNL TITL A STRUCTURAL VIEW OF THE CONSERVED DOMAIN OF RICE JRNL TITL 2 STRESS-RESPONSIVE NAC1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 6368 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.770 REMARK 3 FREE R VALUE TEST SET COUNT : 240 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 32.5096 - 3.2756 1.00 3171 118 0.2209 0.2571 REMARK 3 2 3.2756 - 2.6003 1.00 2957 122 0.2462 0.3339 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 63.39 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.590 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.27630 REMARK 3 B22 (A**2) : 5.27630 REMARK 3 B33 (A**2) : -10.55260 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 : 0.011 1231 REMARK 3 ANGLE : 1.547 1668 REMARK 3 CHIRALITY : 0.118 167 REMARK 3 PLANARITY : 0.007 217 REMARK 3 DIHEDRAL : 19.178 457 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 3ULX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068918. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6435 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 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) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1UT4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 1.5M AMMONIUM SULFATE, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 88.24700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.98600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.98600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.12350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.98600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.98600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 132.37050 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.98600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.98600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.12350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.98600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.98600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 132.37050 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 88.24700 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: 1620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MET A 0 REMARK 465 GLY A 1 REMARK 465 MET A 2 REMARK 465 ARG A 3 REMARK 465 ARG A 4 REMARK 465 GLU A 5 REMARK 465 ARG A 6 REMARK 465 ASP A 7 REMARK 465 LYS A 79 REMARK 465 TYR A 80 REMARK 465 PRO A 81 REMARK 465 ASN A 82 REMARK 465 GLY A 83 REMARK 465 ARG A 144 REMARK 465 ALA A 145 REMARK 465 ALA A 146 REMARK 465 ALA A 147 REMARK 465 GLY A 148 REMARK 465 ALA A 149 REMARK 465 LYS A 150 REMARK 465 LYS A 151 REMARK 465 GLY A 152 REMARK 465 SER A 153 REMARK 465 LEU A 154 REMARK 465 GLU A 170 REMARK 465 TRP A 171 REMARK 465 GLU A 172 REMARK 465 LYS A 173 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 ALA A 142 CB REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 9 -3.92 155.81 REMARK 500 LEU A 12 41.79 -83.00 REMARK 500 ASN A 13 -39.04 -177.66 REMARK 500 HIS A 21 72.53 -156.21 REMARK 500 ARG A 62 -49.91 127.11 REMARK 500 ARG A 76 -111.43 153.52 REMARK 500 ARG A 85 132.99 174.39 REMARK 500 ASN A 87 168.17 100.06 REMARK 500 ARG A 88 105.39 -172.38 REMARK 500 ASN A 92 49.69 -106.28 REMARK 500 PRO A 106 -167.23 -57.18 REMARK 500 ARG A 126 48.54 -85.48 REMARK 500 ALA A 140 78.23 -115.45 REMARK 500 ALA A 142 -108.19 -76.44 REMARK 500 LEU A 156 -140.02 -132.14 REMARK 500 ASP A 157 -79.27 -85.70 REMARK 500 ASP A 158 -54.63 151.23 REMARK 500 TYR A 165 154.05 179.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 9 ALA A 10 143.43 REMARK 500 ASN A 13 LEU A 14 -148.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 3ULX A 0 173 UNP Q27JE5 Q27JE5_ORYSJ 1 174 SEQRES 1 A 174 MET GLY MET ARG ARG GLU ARG ASP ALA GLU ALA GLU LEU SEQRES 2 A 174 ASN LEU PRO PRO GLY PHE ARG PHE HIS PRO THR ASP ASP SEQRES 3 A 174 GLU LEU VAL GLU HIS TYR LEU CYS ARG LYS ALA ALA GLY SEQRES 4 A 174 GLN ARG LEU PRO VAL PRO ILE ILE ALA GLU VAL ASP LEU SEQRES 5 A 174 TYR LYS PHE ASP PRO TRP ASP LEU PRO GLU ARG ALA LEU SEQRES 6 A 174 PHE GLY ALA ARG GLU TRP TYR PHE PHE THR PRO ARG ASP SEQRES 7 A 174 ARG LYS TYR PRO ASN GLY SER ARG PRO ASN ARG ALA ALA SEQRES 8 A 174 GLY ASN GLY TYR TRP LYS ALA THR GLY ALA ASP LYS PRO SEQRES 9 A 174 VAL ALA PRO ARG GLY ARG THR LEU GLY ILE LYS LYS ALA SEQRES 10 A 174 LEU VAL PHE TYR ALA GLY LYS ALA PRO ARG GLY VAL LYS SEQRES 11 A 174 THR ASP TRP ILE MET HIS GLU TYR ARG LEU ALA ASP ALA SEQRES 12 A 174 GLY ARG ALA ALA ALA GLY ALA LYS LYS GLY SER LEU ARG SEQRES 13 A 174 LEU ASP ASP TRP VAL LEU CYS ARG LEU TYR ASN LYS LYS SEQRES 14 A 174 ASN GLU TRP GLU LYS FORMUL 2 HOH *50(H2 O) HELIX 1 1 THR A 23 TYR A 31 1 9 HELIX 2 2 TYR A 31 ALA A 37 1 7 HELIX 3 3 ASP A 50 PHE A 54 5 5 HELIX 4 4 ASP A 55 ALA A 63 5 9 SHEET 1 A 7 ALA A 47 GLU A 48 0 SHEET 2 A 7 GLU A 69 PRO A 75 1 O PHE A 73 N ALA A 47 SHEET 3 A 7 TRP A 159 ASN A 166 -1 O LEU A 164 N TRP A 70 SHEET 4 A 7 VAL A 128 LEU A 139 -1 N ILE A 133 O TYR A 165 SHEET 5 A 7 GLY A 112 ALA A 121 -1 N LEU A 117 O MET A 134 SHEET 6 A 7 GLY A 93 ALA A 97 -1 N TYR A 94 O TYR A 120 SHEET 7 A 7 ARG A 88 ALA A 90 -1 N ARG A 88 O TRP A 95 SHEET 1 B 6 ALA A 47 GLU A 48 0 SHEET 2 B 6 GLU A 69 PRO A 75 1 O PHE A 73 N ALA A 47 SHEET 3 B 6 TRP A 159 ASN A 166 -1 O LEU A 164 N TRP A 70 SHEET 4 B 6 VAL A 128 LEU A 139 -1 N ILE A 133 O TYR A 165 SHEET 5 B 6 GLY A 112 ALA A 121 -1 N LEU A 117 O MET A 134 SHEET 6 B 6 LYS A 102 VAL A 104 -1 N VAL A 104 O GLY A 112 CISPEP 1 GLU A 61 ARG A 62 0 -8.14 CISPEP 2 ALA A 124 PRO A 125 0 -8.63 CISPEP 3 ASP A 157 ASP A 158 0 7.85 CRYST1 45.972 45.972 176.494 90.00 90.00 90.00 P 41 21 2 8 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 0.021752 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021752 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005666 0.00000