HEADER CHAPERONE 24-AUG-12 4GR2 TITLE STRUCTURE OF ATRBCX1 FROM ARABIDOPSIS THALIANA. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATRBCX1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 47-174; COMPND 5 SYNONYM: CHAPERONIN-LIKE RBCX PROTEIN, PUTATIVE UNCHARACTERIZED COMPND 6 PROTEIN AT4G04330; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CHAPERONE, RUBISCO, RBCX EXPDTA X-RAY DIFFRACTION AUTHOR P.GOLIK,P.GRUDNIK,P.KOLESINSKI,G.DUBIN,A.SZCZEPANIAK REVDAT 3 13-SEP-23 4GR2 1 SEQADV REVDAT 2 06-MAR-13 4GR2 1 JRNL REVDAT 1 30-JAN-13 4GR2 0 JRNL AUTH P.KOLESINSKI,P.GOLIK,P.GRUDNIK,J.PIECHOTA,M.MARKIEWICZ, JRNL AUTH 2 M.TARNAWSKI,G.DUBIN,A.SZCZEPANIAK JRNL TITL INSIGHTS INTO EUKARYOTIC RUBISCO ASSEMBLY - CRYSTAL JRNL TITL 2 STRUCTURES OF RBCX CHAPERONES FROM ARABIDOPSIS THALIANA. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1830 2899 2013 JRNL REFN ISSN 0006-3002 JRNL PMID 23295968 JRNL DOI 10.1016/J.BBAGEN.2012.12.025 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1062) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 20069 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1035 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 19.7334 - 3.8175 0.95 2943 140 0.1951 0.2083 REMARK 3 2 3.8175 - 3.0336 0.95 2789 148 0.2069 0.2885 REMARK 3 3 3.0336 - 2.6512 0.95 2706 175 0.2176 0.2879 REMARK 3 4 2.6512 - 2.4092 0.94 2701 154 0.2204 0.2580 REMARK 3 5 2.4092 - 2.2368 0.93 2658 147 0.2140 0.2891 REMARK 3 6 2.2368 - 2.1051 0.93 2640 143 0.2239 0.2790 REMARK 3 7 2.1051 - 2.0000 0.92 2597 128 0.2600 0.3231 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.060 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 : 0.009 1901 REMARK 3 ANGLE : 1.091 2571 REMARK 3 CHIRALITY : 0.075 279 REMARK 3 PLANARITY : 0.004 336 REMARK 3 DIHEDRAL : 13.706 710 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 4GR2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074530. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20075 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 19.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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: 2Z44 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32% ISOPROPANOL, 100 MM MES , PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.45500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.45500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 227 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 TYR A 2 REMARK 465 VAL A 3 REMARK 465 PRO A 4 REMARK 465 GLY A 5 REMARK 465 PHE A 6 REMARK 465 GLY A 7 REMARK 465 GLU A 118 REMARK 465 THR A 119 REMARK 465 SER A 120 REMARK 465 HIS A 121 REMARK 465 VAL A 122 REMARK 465 GLU A 123 REMARK 465 THR A 124 REMARK 465 ASP A 125 REMARK 465 SER A 126 REMARK 465 ASP A 127 REMARK 465 LYS A 128 REMARK 465 MET B 1 REMARK 465 TYR B 2 REMARK 465 HIS B 121 REMARK 465 VAL B 122 REMARK 465 GLU B 123 REMARK 465 THR B 124 REMARK 465 ASP B 125 REMARK 465 SER B 126 REMARK 465 ASP B 127 REMARK 465 LYS B 128 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 GLU A 8 CG CD OE1 OE2 REMARK 470 GLU A 41 CD OE1 OE2 REMARK 470 ARG A 98 CZ NH1 NH2 REMARK 470 LYS A 102 NZ REMARK 470 LEU A 117 CG CD1 CD2 REMARK 470 GLU B 8 CG CD OE1 OE2 REMARK 470 TYR B 38 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU B 41 CG CD OE1 OE2 REMARK 470 MET B 44 CB CG SD CE REMARK 470 LYS B 60 CG CD CE NZ REMARK 470 GLU B 81 CG CD OE1 OE2 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 O HOH A 244 O HOH A 245 2.14 REMARK 500 ND1 HIS B 18 O HOH B 235 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 39 79.86 -158.14 REMARK 500 SER A 69 177.38 178.35 REMARK 500 GLU B 8 -103.54 -127.03 REMARK 500 ASN B 39 73.03 -175.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GR6 RELATED DB: PDB DBREF 4GR2 A 1 128 UNP Q94AU9 Q94AU9_ARATH 47 174 DBREF 4GR2 B 1 128 UNP Q94AU9 Q94AU9_ARATH 47 174 SEQADV 4GR2 LEU A 62 UNP Q94AU9 CYS 108 ENGINEERED MUTATION SEQADV 4GR2 ALA A 87 UNP Q94AU9 CYS 133 ENGINEERED MUTATION SEQADV 4GR2 LEU B 62 UNP Q94AU9 CYS 108 ENGINEERED MUTATION SEQADV 4GR2 ALA B 87 UNP Q94AU9 CYS 133 ENGINEERED MUTATION SEQRES 1 A 128 MET TYR VAL PRO GLY PHE GLY GLU ALA SER PRO GLU ALA SEQRES 2 A 128 LYS ALA ALA LYS HIS LEU HIS ASP PHE PHE THR TYR VAL SEQRES 3 A 128 ALA VAL ARG ILE VAL SER ALA GLN LEU GLU SER TYR ASN SEQRES 4 A 128 PRO GLU ALA TYR MET GLU LEU ARG GLU PHE LEU ASP THR SEQRES 5 A 128 ASN SER VAL SER ASP GLY ASP LYS PHE LEU ALA THR LEU SEQRES 6 A 128 MET ARG ARG SER SER ARG HIS MET ASN LEU ALA LEU ARG SEQRES 7 A 128 ILE LEU GLU VAL ARG SER ALA TYR ALA LYS ASN ASP PHE SEQRES 8 A 128 GLU TRP ASP ASN MET LYS ARG LEU ALA PHE LYS ASN VAL SEQRES 9 A 128 ASP ASP SER ASN THR ARG LEU MET ARG GLU TYR VAL LEU SEQRES 10 A 128 GLU THR SER HIS VAL GLU THR ASP SER ASP LYS SEQRES 1 B 128 MET TYR VAL PRO GLY PHE GLY GLU ALA SER PRO GLU ALA SEQRES 2 B 128 LYS ALA ALA LYS HIS LEU HIS ASP PHE PHE THR TYR VAL SEQRES 3 B 128 ALA VAL ARG ILE VAL SER ALA GLN LEU GLU SER TYR ASN SEQRES 4 B 128 PRO GLU ALA TYR MET GLU LEU ARG GLU PHE LEU ASP THR SEQRES 5 B 128 ASN SER VAL SER ASP GLY ASP LYS PHE LEU ALA THR LEU SEQRES 6 B 128 MET ARG ARG SER SER ARG HIS MET ASN LEU ALA LEU ARG SEQRES 7 B 128 ILE LEU GLU VAL ARG SER ALA TYR ALA LYS ASN ASP PHE SEQRES 8 B 128 GLU TRP ASP ASN MET LYS ARG LEU ALA PHE LYS ASN VAL SEQRES 9 B 128 ASP ASP SER ASN THR ARG LEU MET ARG GLU TYR VAL LEU SEQRES 10 B 128 GLU THR SER HIS VAL GLU THR ASP SER ASP LYS FORMUL 3 HOH *104(H2 O) HELIX 1 1 SER A 10 ASN A 39 1 30 HELIX 2 2 ASN A 39 ASN A 53 1 15 HELIX 3 3 SER A 54 ASP A 57 5 4 HELIX 4 4 GLY A 58 SER A 69 1 12 HELIX 5 5 SER A 69 ASP A 90 1 22 HELIX 6 6 GLU A 92 LEU A 117 1 26 HELIX 7 7 SER B 10 GLU B 36 1 27 HELIX 8 8 ASN B 39 ASN B 53 1 15 HELIX 9 9 ASP B 57 SER B 69 1 13 HELIX 10 10 SER B 69 ASP B 90 1 22 HELIX 11 11 GLU B 92 THR B 119 1 28 CRYST1 45.270 47.640 140.910 90.00 90.00 90.00 P 2 2 21 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 0.022090 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020991 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007097 0.00000