HEADER PHOTOSYNTHESIS 15-FEB-17 5X56 TITLE CRYSTAL STRUCTURE OF PSB27 FROM ARABIDOPSIS THALIANA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTOSYSTEM II REPAIR PROTEIN PSB27-H1, CHLOROPLASTIC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PSB27-H1,THYLAKOID LUMENAL PROTEIN PSB27-H1; COMPND 5 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: PSB27-1, AT1G03600, F21B7.14, F21B7.21, F21B7.22, F21B7_140; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS PHOTOSYNTHESIS PROTEIN, PHOTOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,X.CHENG REVDAT 3 22-NOV-23 5X56 1 REMARK REVDAT 2 25-APR-18 5X56 1 JRNL REVDAT 1 27-DEC-17 5X56 0 JRNL AUTH X.CHENG,J.LIU,Z.HUAN,L.FUDONG,Z.SHUYA,X.MIN,R.KE,W.YUHUA, JRNL AUTH 2 F.AIGEN JRNL TITL CRYSTAL STRUCTURE OF PSB27 FROM ARABIDOPSIS THALIANA JRNL TITL 2 DETERMINED AT A RESOLUTION OF 1.85 ANGSTROM. JRNL REF PHOTOSYN. RES. V. 136 139 2018 JRNL REFN ISSN 1573-5079 JRNL PMID 29098572 JRNL DOI 10.1007/S11120-017-0450-3 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 16080 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.680 REMARK 3 FREE R VALUE TEST SET COUNT : 753 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 39.8184 - 3.1631 0.98 3090 156 0.1915 0.2363 REMARK 3 2 3.1631 - 2.5107 0.99 3114 127 0.2197 0.2508 REMARK 3 3 2.5107 - 2.1934 0.99 3059 172 0.2175 0.2953 REMARK 3 4 2.1934 - 1.9929 0.99 3059 155 0.2242 0.2595 REMARK 3 5 1.9929 - 1.8500 0.98 3005 143 0.2843 0.3565 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.56 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 : 0.007 1619 REMARK 3 ANGLE : 0.796 2183 REMARK 3 CHIRALITY : 0.049 248 REMARK 3 PLANARITY : 0.005 280 REMARK 3 DIHEDRAL : 13.683 1011 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): 59.0425 10.8464 7.9651 REMARK 3 T TENSOR REMARK 3 T11: 0.2083 T22: 0.1876 REMARK 3 T33: 0.1688 T12: -0.0073 REMARK 3 T13: 0.0253 T23: -0.0299 REMARK 3 L TENSOR REMARK 3 L11: 0.2974 L22: 2.8243 REMARK 3 L33: 0.8528 L12: 0.5471 REMARK 3 L13: -0.3844 L23: -1.2831 REMARK 3 S TENSOR REMARK 3 S11: -0.0416 S12: -0.0020 S13: -0.0202 REMARK 3 S21: 0.0107 S22: -0.0048 S23: -0.0125 REMARK 3 S31: -0.0008 S32: -0.0182 S33: 0.0458 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 5X56 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1300002940. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16102 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 49.113 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07900 REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : 0.57000 REMARK 200 FOR SHELL : 1.200 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: 2Y6X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M POTASSIUM/SODIUM PHOSPHATE PH 7.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 43.13000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 43.13000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.20000 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 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 B 226 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 ALA A 1 REMARK 465 GLU A 2 REMARK 465 ASP A 3 REMARK 465 ALA B 1 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 GLN A 24 CG CD OE1 NE2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 THR A 103 OG1 CG2 REMARK 470 ARG A 104 CG CD NE CZ NH1 NH2 REMARK 470 THR B 26 OG1 CG2 REMARK 470 LYS B 52 CG CD CE NZ 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 ASP B 27 129.84 -27.50 REMARK 500 ASN B 29 1.68 -68.61 REMARK 500 REMARK 500 REMARK: NULL DBREF 5X56 A 1 106 UNP Q9LR64 PB27A_ARATH 69 174 DBREF 5X56 B 1 106 UNP Q9LR64 PB27A_ARATH 69 174 SEQRES 1 A 106 ALA GLU ASP GLU GLU TYR ILE LYS ASP THR SER ALA VAL SEQRES 2 A 106 ILE SER LYS VAL ARG SER THR LEU SER MET GLN LYS THR SEQRES 3 A 106 ASP PRO ASN VAL ALA ASP ALA VAL ALA GLU LEU ARG GLU SEQRES 4 A 106 ALA SER ASN SER TRP VAL ALA LYS TYR ARG LYS GLU LYS SEQRES 5 A 106 ALA LEU LEU GLY LYS ALA SER PHE ARG ASP ILE TYR SER SEQRES 6 A 106 ALA LEU ASN ALA VAL SER GLY HIS TYR VAL SER PHE GLY SEQRES 7 A 106 PRO THR ALA PRO ILE PRO ALA LYS ARG LYS ALA ARG ILE SEQRES 8 A 106 LEU GLU GLU MET GLU THR ALA GLU LYS ALA LEU THR ARG SEQRES 9 A 106 GLY ARG SEQRES 1 B 106 ALA GLU ASP GLU GLU TYR ILE LYS ASP THR SER ALA VAL SEQRES 2 B 106 ILE SER LYS VAL ARG SER THR LEU SER MET GLN LYS THR SEQRES 3 B 106 ASP PRO ASN VAL ALA ASP ALA VAL ALA GLU LEU ARG GLU SEQRES 4 B 106 ALA SER ASN SER TRP VAL ALA LYS TYR ARG LYS GLU LYS SEQRES 5 B 106 ALA LEU LEU GLY LYS ALA SER PHE ARG ASP ILE TYR SER SEQRES 6 B 106 ALA LEU ASN ALA VAL SER GLY HIS TYR VAL SER PHE GLY SEQRES 7 B 106 PRO THR ALA PRO ILE PRO ALA LYS ARG LYS ALA ARG ILE SEQRES 8 B 106 LEU GLU GLU MET GLU THR ALA GLU LYS ALA LEU THR ARG SEQRES 9 B 106 GLY ARG FORMUL 3 HOH *49(H2 O) HELIX 1 AA1 GLU A 4 SER A 22 1 19 HELIX 2 AA2 ASN A 29 ARG A 49 1 21 HELIX 3 AA3 LYS A 52 GLY A 56 5 5 HELIX 4 AA4 LYS A 57 PHE A 77 1 21 HELIX 5 AA5 PRO A 84 THR A 103 1 20 HELIX 6 AA6 ASP B 3 SER B 22 1 20 HELIX 7 AA7 ASN B 29 ARG B 49 1 21 HELIX 8 AA8 GLU B 51 GLY B 56 5 6 HELIX 9 AA9 LYS B 57 GLY B 78 1 22 HELIX 10 AB1 PRO B 84 THR B 103 1 20 CRYST1 86.260 62.400 38.960 90.00 112.63 90.00 C 1 2 1 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 0.011593 0.000000 0.004833 0.00000 SCALE2 0.000000 0.016026 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027808 0.00000