HEADER PHOTOSYNTHESIS 28-JUN-10 3NPH TITLE CRYSTAL STRUCTURE OF THE PFAM00427 DOMAIN FROM SYNECHOCYSTIS SP. PCC TITLE 2 6803 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHYCOBILISOME 32.1 KDA LINKER POLYPEPTIDE, PHYCOCYANIN- COMPND 3 ASSOCIATED, ROD 2; COMPND 4 CHAIN: B; COMPND 5 FRAGMENT: PFAM00427 DOMAIN, PBS-LINKER, UNP RESIDUES 19-157; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP.; SOURCE 3 ORGANISM_TAXID: 1148; SOURCE 4 STRAIN: PCC 6803; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DH3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS PFAM00427 DOMAIN, LINKER PROTEIN, PHYCOBILIPROTEIN, PHOTOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR X.GAO,L.CHEN,J.-W.WU,Y.-Z.ZHANG REVDAT 3 14-DEC-11 3NPH 1 JRNL REVDAT 2 19-OCT-11 3NPH 1 JRNL VERSN REVDAT 1 29-JUN-11 3NPH 0 JRNL AUTH X.GAO,N.ZHANG,T.-D.WEI,H.-N.SU,B.-B.XIE,C.-C.DONG, JRNL AUTH 2 X.-Y.ZHANG,X.-L.CHEN,B.-C.ZHOU,Z.-X.WANG,J.-W.WU,Y.-Z.ZHANG JRNL TITL CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF LINKER L(R) JRNL TITL 2 AND THE ASSEMBLY OF CYANOBACTERIAL PHYCOBILISOME RODS JRNL REF MOL.MICROBIOL. V. 82 698 2011 JRNL REFN ISSN 0950-382X JRNL PMID 21923764 JRNL DOI 10.1111/J.1365-2958.2011.07844.X REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 11164 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1117 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 22.7741 - 3.6929 1.00 1361 152 0.2090 0.2462 REMARK 3 2 3.6929 - 2.9331 1.00 1273 141 0.2036 0.2551 REMARK 3 3 2.9331 - 2.5629 1.00 1262 140 0.2260 0.3090 REMARK 3 4 2.5629 - 2.3288 1.00 1237 138 0.2211 0.2415 REMARK 3 5 2.3288 - 2.1621 1.00 1246 139 0.2129 0.2651 REMARK 3 6 2.1621 - 2.0347 1.00 1229 136 0.2122 0.2894 REMARK 3 7 2.0347 - 1.9328 1.00 1221 135 0.2126 0.3142 REMARK 3 8 1.9328 - 1.8487 0.99 1218 136 0.2199 0.2720 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 : 0.36 REMARK 3 B_SOL : 62.70 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.85440 REMARK 3 B22 (A**2) : -5.85440 REMARK 3 B33 (A**2) : 2.40440 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 1116 REMARK 3 ANGLE : 0.988 1510 REMARK 3 CHIRALITY : 0.073 158 REMARK 3 PLANARITY : 0.004 200 REMARK 3 DIHEDRAL : 18.479 402 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 3NPH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUL-10. REMARK 100 THE RCSB ID CODE IS RCSB060116. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 FR-E+ DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.498 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11164 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.849 REMARK 200 RESOLUTION RANGE LOW (A) : 39.430 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) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 3000, 0.1M BIS-TRIS BUFFER (PH REMARK 280 6.5), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 39.59350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.83750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.83750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.79675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.83750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.83750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.39025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.83750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.83750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 19.79675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.83750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.83750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 59.39025 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 39.59350 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: 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 185 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 208 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 231 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 B 1 REMARK 465 ILE B 2 REMARK 465 PRO B 3 REMARK 465 LEU B 4 REMARK 465 GLY B 136 REMARK 465 PHE B 137 REMARK 465 ALA B 138 REMARK 465 THR B 139 REMARK 465 GLN B 140 REMARK 465 LEU B 141 REMARK 465 GLU B 142 REMARK 465 HIS B 143 REMARK 465 HIS B 144 REMARK 465 HIS B 145 REMARK 465 HIS B 146 REMARK 465 HIS B 147 REMARK 465 HIS B 148 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 SER B 10 O THR B 11 1.71 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 ARG B 7 -131.10 -56.91 REMARK 500 SER B 8 -145.36 110.47 REMARK 500 SER B 10 -38.58 -169.73 REMARK 500 THR B 11 178.57 30.39 REMARK 500 GLU B 12 -76.43 103.28 REMARK 500 PHE B 70 -60.73 -96.54 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 SER B 10 THR B 11 134.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 276 DISTANCE = 5.45 ANGSTROMS DBREF 3NPH B 2 140 UNP P73204 PYR2_SYNY3 19 157 SEQADV 3NPH MET B 1 UNP P73204 EXPRESSION TAG SEQADV 3NPH LEU B 141 UNP P73204 EXPRESSION TAG SEQADV 3NPH GLU B 142 UNP P73204 EXPRESSION TAG SEQADV 3NPH HIS B 143 UNP P73204 EXPRESSION TAG SEQADV 3NPH HIS B 144 UNP P73204 EXPRESSION TAG SEQADV 3NPH HIS B 145 UNP P73204 EXPRESSION TAG SEQADV 3NPH HIS B 146 UNP P73204 EXPRESSION TAG SEQADV 3NPH HIS B 147 UNP P73204 EXPRESSION TAG SEQADV 3NPH HIS B 148 UNP P73204 EXPRESSION TAG SEQRES 1 B 148 MET ILE PRO LEU GLU LEU ARG SER ARG SER THR GLU GLU SEQRES 2 B 148 GLU VAL ASP ALA VAL ILE LEU ALA VAL TYR ARG GLN VAL SEQRES 3 B 148 LEU GLY ASN ASP HIS LEU MET SER GLN GLU ARG LEU THR SEQRES 4 B 148 SER ALA GLU SER LEU LEU ARG GLY ARG GLU ILE SER VAL SEQRES 5 B 148 ARG ASP PHE VAL ARG ALA VAL ALA LEU SER GLU VAL TYR SEQRES 6 B 148 ARG GLN LYS PHE PHE HIS SER ASN PRO GLN ASN ARG PHE SEQRES 7 B 148 ILE GLU LEU ASN TYR LYS HIS LEU LEU GLY ARG ALA PRO SEQRES 8 B 148 TYR ASP GLN SER GLU ILE ALA PHE HIS THR ASP LEU TYR SEQRES 9 B 148 HIS GLN GLY GLY TYR GLU ALA GLU ILE ASN SER TYR ILE SEQRES 10 B 148 ASP SER VAL GLU TYR THR GLU ASN PHE GLY ASP TRP VAL SEQRES 11 B 148 VAL PRO TYR PHE ARG GLY PHE ALA THR GLN LEU GLU HIS SEQRES 12 B 148 HIS HIS HIS HIS HIS FORMUL 2 HOH *141(H2 O) HELIX 1 1 GLU B 12 GLY B 28 1 17 HELIX 2 2 LEU B 38 GLY B 47 1 10 HELIX 3 3 SER B 51 LEU B 61 1 11 HELIX 4 4 SER B 62 PHE B 70 1 9 HELIX 5 5 PRO B 74 LEU B 87 1 14 HELIX 6 6 ASP B 93 GLY B 108 1 16 HELIX 7 7 GLY B 108 ASP B 118 1 11 HELIX 8 8 SER B 119 PHE B 126 1 8 CRYST1 55.675 55.675 79.187 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 0.017961 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017961 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012628 0.00000 MASTER 305 0 0 8 0 0 0 6 0 0 0 12 END