HEADER CHAPERONE 04-JUL-15 5CDK TITLE APICAL DOMAIN OF CHLOROPLAST CHAPERONIN 60B1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAPERONIN 60B1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: APICAL-DOMAIN, UNP RESIDUES 223-404; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHLAMYDOMONAS REINHARDTII; SOURCE 3 ORGANISM_TAXID: 3055; SOURCE 4 GENE: CPN60B1, CHLREDRAFT_132530; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS APICAL DOMAIN CPN60B1, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR S.ZHANG,F.YU,C.LIU,F.GAO REVDAT 4 20-MAR-24 5CDK 1 REMARK REVDAT 3 04-OCT-17 5CDK 1 REMARK REVDAT 2 17-MAY-17 5CDK 1 JRNL REVDAT 1 13-JUL-16 5CDK 0 JRNL AUTH S.ZHANG,H.ZHOU,F.YU,F.GAO,J.HE,C.LIU JRNL TITL FUNCTIONAL PARTITION OF CPN60 ALPHA AND CPN60 BETA SUBUNITS JRNL TITL 2 IN SUBSTRATE RECOGNITION AND COOPERATION WITH CO-CHAPERONINS JRNL REF MOL PLANT V. 9 1210 2016 JRNL REFN ESSN 1752-9867 JRNL PMID 27179919 JRNL DOI 10.1016/J.MOLP.2016.04.019 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 28598 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1486 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 31.5580 - 3.3341 0.96 2695 153 0.1782 0.1572 REMARK 3 2 3.3341 - 2.6468 1.00 2629 151 0.1582 0.1569 REMARK 3 3 2.6468 - 2.3124 1.00 2639 135 0.1437 0.1723 REMARK 3 4 2.3124 - 2.1010 1.00 2592 139 0.1284 0.1653 REMARK 3 5 2.1010 - 1.9504 1.00 2603 143 0.1214 0.1744 REMARK 3 6 1.9504 - 1.8354 1.00 2618 109 0.1142 0.1897 REMARK 3 7 1.8354 - 1.7435 1.00 2594 118 0.1116 0.1939 REMARK 3 8 1.7435 - 1.6676 1.00 2570 142 0.1018 0.1706 REMARK 3 9 1.6676 - 1.6034 1.00 2550 139 0.0979 0.1591 REMARK 3 10 1.6034 - 1.5481 1.00 2588 131 0.0942 0.1752 REMARK 3 11 1.5481 - 1.4997 0.99 2518 126 0.0923 0.1649 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.210 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 : 0.018 1434 REMARK 3 ANGLE : 1.622 1941 REMARK 3 CHIRALITY : 0.081 236 REMARK 3 PLANARITY : 0.009 250 REMARK 3 DIHEDRAL : 13.627 556 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 5CDK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211444. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.5 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30082 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 31.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.8000 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: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M CALCIUM CHLORIDE DEHYDRATE, 0.1 REMARK 280 M BIS-TRIS PH 6.5, 30% V/V POLYETHYLENE GLYCOL MONOMETHYL ETHER REMARK 280 550, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 31.93300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.37850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.93300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.37850 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: MONOMERIC 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 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 GLY A 182 REMARK 465 GLY A 183 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 324 O HOH A 345 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 26 CB CYS A 26 SG -0.105 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 93 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES 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 ASP A 32 52.13 -90.90 REMARK 500 GLU A 112 -56.72 84.00 REMARK 500 MET A 113 98.91 -62.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CDI RELATED DB: PDB REMARK 900 RELATED ID: 5CDJ RELATED DB: PDB DBREF 5CDK A 2 183 UNP A8JE91 A8JE91_CHLRE 223 404 SEQADV 5CDK SER A 1 UNP A8JE91 EXPRESSION TAG SEQRES 1 A 183 SER GLN PHE GLU ARG GLY TYR THR SER PRO TYR PHE VAL SEQRES 2 A 183 THR ASP PRO GLU ARG MET ILE CYS GLU TYR GLU ASN CYS SEQRES 3 A 183 LYS ILE LEU LEU VAL ASP LYS LYS ILE SER THR ALA ARG SEQRES 4 A 183 ASP ILE ILE THR ILE LEU GLU SER ALA ILE ARG GLY ASN SEQRES 5 A 183 TYR PRO LEU LEU ILE MET ALA GLU GLU VAL GLU GLN GLU SEQRES 6 A 183 ALA LEU ALA THR LEU VAL VAL ASN LYS LEU ARG GLY THR SEQRES 7 A 183 LEU LYS VAL VAL ALA ILE LYS ALA PRO GLY PHE GLY GLU SEQRES 8 A 183 ARG ARG SER SER TYR LEU GLU ASP ILE ALA ILE LEU THR SEQRES 9 A 183 GLY GLY THR VAL VAL ARG ASP GLU MET GLY VAL SER LEU SEQRES 10 A 183 GLU GLN ALA THR ASP ALA VAL LEU GLY THR ALA ALA LYS SEQRES 11 A 183 ILE THR ILE THR LYS GLU ARG THR THR VAL VAL GLY ASP SEQRES 12 A 183 GLY SER THR ALA ALA ASP VAL ALA ALA ARG VAL LYS GLN SEQRES 13 A 183 ILE ARG ASN LEU GLN MET GLN THR ASP GLN ASP TYR GLU SEQRES 14 A 183 ARG GLU LYS LEU GLN GLU ARG ILE ALA ARG LEU SER GLY SEQRES 15 A 183 GLY FORMUL 2 HOH *192(H2 O) HELIX 1 AA1 SER A 9 VAL A 13 5 5 HELIX 2 AA2 THR A 37 ASP A 40 5 4 HELIX 3 AA3 ILE A 41 GLY A 51 1 11 HELIX 4 AA4 GLU A 63 ARG A 76 1 14 HELIX 5 AA5 PHE A 89 GLY A 105 1 17 HELIX 6 AA6 THR A 121 LEU A 125 5 5 HELIX 7 AA7 THR A 146 GLN A 163 1 18 HELIX 8 AA8 GLN A 166 SER A 181 1 16 SHEET 1 AA1 6 GLN A 2 PHE A 3 0 SHEET 2 AA1 6 THR A 138 GLY A 142 -1 O THR A 138 N PHE A 3 SHEET 3 AA1 6 GLY A 126 ILE A 133 -1 N LYS A 130 O VAL A 141 SHEET 4 AA1 6 CYS A 21 ILE A 35 -1 N CYS A 21 O ILE A 133 SHEET 5 AA1 6 LEU A 55 VAL A 62 1 O MET A 58 N LEU A 29 SHEET 6 AA1 6 VAL A 81 LYS A 85 1 O VAL A 82 N ILE A 57 SHEET 1 AA2 5 GLN A 2 PHE A 3 0 SHEET 2 AA2 5 THR A 138 GLY A 142 -1 O THR A 138 N PHE A 3 SHEET 3 AA2 5 GLY A 126 ILE A 133 -1 N LYS A 130 O VAL A 141 SHEET 4 AA2 5 CYS A 21 ILE A 35 -1 N CYS A 21 O ILE A 133 SHEET 5 AA2 5 VAL A 109 ARG A 110 1 O VAL A 109 N ASP A 32 CRYST1 63.866 90.757 31.551 90.00 90.00 90.00 P 21 21 2 4 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 0.015658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011018 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031695 0.00000