HEADER PHOTOSYNTHESIS 16-APR-13 4K7B TITLE CRYSTAL STRUCTURE OF EXTRINSIC PROTEIN IN PHOTOSYSTEM II COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXTRINSIC PROTEIN IN PHOTOSYSTEM II; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 56-179; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHAETOCEROS GRACILIS; SOURCE 3 ORGANISM_TAXID: 184592; SOURCE 4 GENE: PSB31; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOTOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR R.NAGAO,M.SUGA,A.NIIKURA,A.OKUMURA,F.H.M.KOUA,T.SUZUKI,T.TOMO, AUTHOR 2 I.ENAMI,J.R.SHEN REVDAT 3 20-MAR-24 4K7B 1 REMARK REVDAT 2 16-OCT-13 4K7B 1 JRNL REVDAT 1 18-SEP-13 4K7B 0 JRNL AUTH R.NAGAO,M.SUGA,A.NIIKURA,A.OKUMURA,F.H.KOUA,T.SUZUKI,T.TOMO, JRNL AUTH 2 I.ENAMI,J.R.SHEN JRNL TITL CRYSTAL STRUCTURE OF PSB31, A NOVEL EXTRINSIC PROTEIN OF JRNL TITL 2 PHOTOSYSTEM II FROM A MARINE CENTRIC DIATOM AND IMPLICATIONS JRNL TITL 3 FOR ITS BINDING AND FUNCTION JRNL REF BIOCHEMISTRY V. 52 6646 2013 JRNL REFN ISSN 0006-2960 JRNL PMID 23988112 JRNL DOI 10.1021/BI400770D REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.940 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 22426 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1118 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 30.2543 - 3.0990 0.99 2756 130 0.1827 0.1709 REMARK 3 2 3.0990 - 2.4601 1.00 2711 129 0.1896 0.1935 REMARK 3 3 2.4601 - 2.1493 1.00 2665 144 0.1763 0.2199 REMARK 3 4 2.1493 - 1.9528 1.00 2597 157 0.1809 0.1863 REMARK 3 5 1.9528 - 1.8128 1.00 2680 143 0.1769 0.2022 REMARK 3 6 1.8128 - 1.7060 1.00 2653 151 0.1917 0.2397 REMARK 3 7 1.7060 - 1.6205 1.00 2624 140 0.2046 0.2260 REMARK 3 8 1.6205 - 1.5500 1.00 2622 124 0.2208 0.2207 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.38 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 : 0.007 906 REMARK 3 ANGLE : 1.166 1230 REMARK 3 CHIRALITY : 0.077 131 REMARK 3 PLANARITY : 0.005 163 REMARK 3 DIHEDRAL : 11.744 345 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): 42.9653 -13.5112 -13.9442 REMARK 3 T TENSOR REMARK 3 T11: 0.1467 T22: 0.0697 REMARK 3 T33: 0.0909 T12: 0.0243 REMARK 3 T13: -0.0131 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 1.1185 L22: 0.7536 REMARK 3 L33: 1.0240 L12: 0.5905 REMARK 3 L13: -0.2969 L23: -0.0043 REMARK 3 S TENSOR REMARK 3 S11: 0.0715 S12: 0.0414 S13: 0.0147 REMARK 3 S21: 0.0547 S22: -0.0390 S23: 0.0000 REMARK 3 S31: -0.0988 S32: -0.0939 S33: -0.0252 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 4K7B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078981. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22604 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.547 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.49900 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: SIRAS, MOLECULAR REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, SHELX, SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 10.42767 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 20.85533 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 20.85533 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 10.42767 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: 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 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 361 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 380 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 ASP A 1 REMARK 465 GLY A 2 REMARK 465 SER A 114 REMARK 465 ARG A 115 REMARK 465 THR A 116 REMARK 465 LYS A 117 REMARK 465 ALA A 118 REMARK 465 GLY A 119 REMARK 465 ALA A 120 REMARK 465 ILE A 121 REMARK 465 TYR A 122 REMARK 465 VAL A 123 REMARK 465 ARG A 124 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 97 CG CD OE1 OE2 REMARK 470 ILE A 98 CG1 CG2 CD1 REMARK 470 ASN A 99 CG OD1 ND2 REMARK 470 SER A 100 OG 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 SER A 100 47.75 -74.87 REMARK 500 REMARK 500 REMARK: NULL 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 203 DBREF 4K7B A 1 124 UNP B6ZHE7 B6ZHE7_9STRA 56 179 SEQRES 1 A 124 ASP GLY ALA VAL SER SER ALA THR ILE ASN ARG ALA ARG SEQRES 2 A 124 GLY LEU TYR GLY ASP ARG ILE ALA ALA LEU LYS ASP ALA SEQRES 3 A 124 VAL ALA ALA GLY ASP PHE LYS ALA ILE ALA GLU GLU LYS SEQRES 4 A 124 ASN ALA PHE ILE LEU PHE ASN SER GLY ALA TYR PRO THR SEQRES 5 A 124 ASN LYS ALA LYS LYS ASN ALA ALA ILE ALA GLN THR ASN SEQRES 6 A 124 GLU ILE PHE LYS ALA ILE ARG SER GLY ASP LYS ALA ALA SEQRES 7 A 124 VAL LYS SER ALA TYR ASP ALA TYR MET ALA ALA ASN GLU SEQRES 8 A 124 ILE ARG PRO LEU PRO GLU ILE ASN SER ASN VAL GLY GLN SEQRES 9 A 124 GLY TYR SER SER GLU PHE ASP PHE ARG SER ARG THR LYS SEQRES 10 A 124 ALA GLY ALA ILE TYR VAL ARG HET SO4 A 201 5 HET SO4 A 202 5 HET GOL A 203 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *99(H2 O) HELIX 1 1 SER A 5 ALA A 22 1 18 HELIX 2 2 LEU A 23 GLY A 30 1 8 HELIX 3 3 ASP A 31 GLU A 38 1 8 HELIX 4 4 GLU A 38 TYR A 50 1 13 HELIX 5 5 ASN A 53 GLY A 74 1 22 HELIX 6 6 ASP A 75 ASN A 90 1 16 HELIX 7 7 SER A 107 ARG A 113 1 7 SITE 1 AC1 5 ALA A 49 TYR A 50 PRO A 51 THR A 52 SITE 2 AC1 5 ASN A 53 SITE 1 AC2 7 ARG A 19 PHE A 32 LYS A 33 ASN A 40 SITE 2 AC2 7 ARG A 113 HOH A 318 HOH A 383 SITE 1 AC3 7 ALA A 55 LYS A 56 ARG A 93 SER A 107 SITE 2 AC3 7 SER A 108 GLU A 109 HOH A 337 CRYST1 92.411 92.411 31.283 90.00 90.00 120.00 P 31 2 1 6 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 0.010821 0.006248 0.000000 0.00000 SCALE2 0.000000 0.012495 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031966 0.00000