HEADER STRUCTURAL PROTEIN 20-MAY-24 8ZLH TITLE THE CRYSTAL STRUCTURE OF CCMS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALL1292 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CCMS; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOSTOC SP. PCC 7120 = FACHB-418; SOURCE 3 ORGANISM_TAXID: 103690; SOURCE 4 GENE: ALL1292; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DIMER, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.CHENG,C.L.LI REVDAT 3 11-SEP-24 8ZLH 1 TITLE REVDAT 2 04-SEP-24 8ZLH 1 JRNL REVDAT 1 28-AUG-24 8ZLH 0 JRNL AUTH J.CHENG,C.Y.LI,M.MENG,J.X.LI,S.J.LIU,H.Y.CAO,N.WANG, JRNL AUTH 2 Y.Z.ZHANG,L.N.LIU JRNL TITL MOLECULAR INTERACTIONS OF THE CHAPERONE CCMS AND CARBOXYSOME JRNL TITL 2 SHELL PROTEIN CCMK1 THAT MEDIATE BETA-CARBOXYSOME ASSEMBLY. JRNL REF PLANT PHYSIOL. 2024 JRNL REFN ESSN 1532-2548 JRNL PMID 39172695 JRNL DOI 10.1093/PLPHYS/KIAE438 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 20247 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.880 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 30.6400 - 4.7900 1.00 1417 155 0.1847 0.2508 REMARK 3 2 4.7800 - 3.8000 1.00 1340 147 0.1635 0.2039 REMARK 3 3 3.8000 - 3.3200 1.00 1322 145 0.1850 0.2175 REMARK 3 4 3.3200 - 3.0100 1.00 1302 143 0.2099 0.2584 REMARK 3 5 3.0100 - 2.8000 1.00 1311 143 0.2181 0.2748 REMARK 3 6 2.8000 - 2.6300 1.00 1291 142 0.2196 0.2660 REMARK 3 7 2.6300 - 2.5000 1.00 1280 140 0.2132 0.2779 REMARK 3 8 2.5000 - 2.3900 1.00 1291 141 0.2086 0.2577 REMARK 3 9 2.3900 - 2.3000 1.00 1282 141 0.2018 0.2786 REMARK 3 10 2.3000 - 2.2200 1.00 1296 143 0.1986 0.2847 REMARK 3 11 2.2200 - 2.1500 1.00 1281 139 0.2106 0.2290 REMARK 3 12 2.1500 - 2.0900 1.00 1298 142 0.2270 0.2879 REMARK 3 13 2.0900 - 2.0400 1.00 1235 136 0.2378 0.2989 REMARK 3 14 2.0400 - 1.9900 1.00 1301 143 0.2795 0.3131 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 26.550 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 : 0.010 NULL REMARK 3 ANGLE : 1.145 NULL REMARK 3 CHIRALITY : 0.074 316 REMARK 3 PLANARITY : 0.010 388 REMARK 3 DIHEDRAL : 6.076 272 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): 6.5631 5.1121 12.9251 REMARK 3 T TENSOR REMARK 3 T11: 0.2463 T22: 0.2018 REMARK 3 T33: 0.2533 T12: 0.0088 REMARK 3 T13: -0.0035 T23: 0.0139 REMARK 3 L TENSOR REMARK 3 L11: 1.0960 L22: 0.5938 REMARK 3 L33: 2.4441 L12: 0.1576 REMARK 3 L13: 0.3790 L23: 0.1120 REMARK 3 S TENSOR REMARK 3 S11: -0.0177 S12: -0.0111 S13: -0.0508 REMARK 3 S21: -0.0144 S22: 0.0129 S23: 0.0055 REMARK 3 S31: 0.0500 S32: 0.0169 S33: -0.0000 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 8ZLH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 22-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1300047990. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20318 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 35.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM FORMATE, 20% W/V PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.26800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.78500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.31350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.78500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.26800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.31350 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: 1840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 MET A 2 REMARK 465 PHE A 3 REMARK 465 GLY A 4 REMARK 465 SER A 5 REMARK 465 THR A 6 REMARK 465 LYS A 7 REMARK 465 PRO A 8 REMARK 465 GLU A 9 REMARK 465 SER A 10 REMARK 465 GLY A 11 REMARK 465 ASP A 12 REMARK 465 MET B 1 REMARK 465 MET B 2 REMARK 465 PHE B 3 REMARK 465 GLY B 4 REMARK 465 SER B 5 REMARK 465 THR B 6 REMARK 465 LYS B 7 REMARK 465 PRO B 8 REMARK 465 GLU B 9 REMARK 465 SER B 10 REMARK 465 GLY B 11 REMARK 465 ASP B 12 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 71 32.30 -72.90 REMARK 500 ASN A 75 -104.51 -115.56 REMARK 500 ASN B 75 -103.25 -107.37 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 278 DISTANCE = 5.81 ANGSTROMS DBREF 8ZLH A 1 142 UNP Q8YXC3 Q8YXC3_NOSS1 1 142 DBREF 8ZLH B 1 142 UNP Q8YXC3 Q8YXC3_NOSS1 1 142 SEQRES 1 A 142 MET MET PHE GLY SER THR LYS PRO GLU SER GLY ASP SER SEQRES 2 A 142 LYS TRP ARG SER GLN LEU ASP ARG PHE VAL LYS GLU ASN SEQRES 3 A 142 GLN GLN ASP LEU ALA ALA LEU PHE TRP GLY LEU TRP LEU SEQRES 4 A 142 GLU ASN GLY ASP SER GLN GLY THR ILE GLY ILE ASP LEU SEQRES 5 A 142 GLN PRO THR PRO HIS PHE VAL TYR CYS PRO LYS ASP ALA SEQRES 6 A 142 VAL GLU LYS LEU ASN ASN ASN VAL GLU ASN ARG LEU GLN SEQRES 7 A 142 GLU LEU LEU GLY ILE ILE GLU HIS ASN GLN PRO GLU ILE SEQRES 8 A 142 GLU VAL LEU MET ILE GLY ILE GLY LYS GLY GLU ILE LYS SEQRES 9 A 142 LEU ILE GLN PHE ALA PRO GLU PRO PRO PRO PRO VAL CYS SEQRES 10 A 142 PHE GLU GLN VAL GLY LYS ASP ILE ASP GLY LEU LEU GLU SEQRES 11 A 142 LEU LEU GLU GLN ARG MET SER GLY GLU ILE VAL VAL SEQRES 1 B 142 MET MET PHE GLY SER THR LYS PRO GLU SER GLY ASP SER SEQRES 2 B 142 LYS TRP ARG SER GLN LEU ASP ARG PHE VAL LYS GLU ASN SEQRES 3 B 142 GLN GLN ASP LEU ALA ALA LEU PHE TRP GLY LEU TRP LEU SEQRES 4 B 142 GLU ASN GLY ASP SER GLN GLY THR ILE GLY ILE ASP LEU SEQRES 5 B 142 GLN PRO THR PRO HIS PHE VAL TYR CYS PRO LYS ASP ALA SEQRES 6 B 142 VAL GLU LYS LEU ASN ASN ASN VAL GLU ASN ARG LEU GLN SEQRES 7 B 142 GLU LEU LEU GLY ILE ILE GLU HIS ASN GLN PRO GLU ILE SEQRES 8 B 142 GLU VAL LEU MET ILE GLY ILE GLY LYS GLY GLU ILE LYS SEQRES 9 B 142 LEU ILE GLN PHE ALA PRO GLU PRO PRO PRO PRO VAL CYS SEQRES 10 B 142 PHE GLU GLN VAL GLY LYS ASP ILE ASP GLY LEU LEU GLU SEQRES 11 B 142 LEU LEU GLU GLN ARG MET SER GLY GLU ILE VAL VAL FORMUL 3 HOH *155(H2 O) HELIX 1 AA1 LYS A 14 ASN A 26 1 13 HELIX 2 AA2 ASN A 26 GLY A 42 1 17 HELIX 3 AA3 PRO A 62 ASN A 71 1 10 HELIX 4 AA4 GLU A 79 ASN A 87 1 9 HELIX 5 AA5 PRO A 113 GLY A 122 1 10 HELIX 6 AA6 ASP A 124 SER A 137 1 14 HELIX 7 AA7 LYS B 14 ASN B 26 1 13 HELIX 8 AA8 ASN B 26 GLY B 42 1 17 HELIX 9 AA9 PRO B 62 ASN B 71 1 10 HELIX 10 AB1 GLU B 79 ASN B 87 1 9 HELIX 11 AB2 PRO B 113 GLY B 122 1 10 HELIX 12 AB3 ASP B 124 SER B 137 1 14 SHEET 1 AA1 4 HIS A 57 CYS A 61 0 SHEET 2 AA1 4 THR A 47 ASP A 51 -1 N GLY A 49 O VAL A 59 SHEET 3 AA1 4 VAL A 93 GLY A 99 1 O ILE A 96 N ILE A 50 SHEET 4 AA1 4 GLU A 102 PHE A 108 -1 O GLU A 102 N GLY A 99 SHEET 1 AA2 4 HIS B 57 CYS B 61 0 SHEET 2 AA2 4 THR B 47 ASP B 51 -1 N THR B 47 O CYS B 61 SHEET 3 AA2 4 VAL B 93 GLY B 99 1 O ILE B 96 N ILE B 50 SHEET 4 AA2 4 GLU B 102 PHE B 108 -1 O PHE B 108 N VAL B 93 CISPEP 1 GLN A 53 PRO A 54 0 3.73 CISPEP 2 GLU A 111 PRO A 112 0 -9.35 CISPEP 3 GLN B 53 PRO B 54 0 3.84 CISPEP 4 GLU B 111 PRO B 112 0 -4.38 CRYST1 40.536 74.627 93.570 90.00 90.00 90.00 P 21 21 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 0.024669 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013400 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010687 0.00000