HEADER STRUCTURAL PROTEIN 21-MAY-24 8ZLZ TITLE THE COMPLEX CRYSTAL STRUCTURE OF CCMS AND C-TERMINUS OF CCMK1. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALL1292 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: C-TERMINUS OF CCMK1; COMPND 7 CHAIN: D; COMPND 8 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; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: NOSTOC SP. PCC 7120 = FACHB-418; SOURCE 9 ORGANISM_TAXID: 103690; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COMPLEX, CCMS, CCMK1, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.CHENG,C.Y.LI REVDAT 2 04-SEP-24 8ZLZ 1 JRNL REVDAT 1 28-AUG-24 8ZLZ 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. 1.67 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 32194 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.210 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 34.0100 - 4.0100 1.00 2388 159 0.1763 0.1977 REMARK 3 2 4.0100 - 3.1900 1.00 2252 148 0.1652 0.1942 REMARK 3 3 3.1800 - 2.7800 1.00 2232 148 0.1865 0.2214 REMARK 3 4 2.7800 - 2.5300 1.00 2189 145 0.1928 0.2299 REMARK 3 5 2.5300 - 2.3500 1.00 2193 145 0.1820 0.2391 REMARK 3 6 2.3500 - 2.2100 1.00 2191 146 0.1807 0.2001 REMARK 3 7 2.2100 - 2.1000 1.00 2166 143 0.1727 0.2150 REMARK 3 8 2.1000 - 2.0100 1.00 2161 144 0.1751 0.2135 REMARK 3 9 2.0100 - 1.9300 1.00 2153 142 0.1814 0.2249 REMARK 3 10 1.9300 - 1.8600 1.00 2144 142 0.1926 0.2476 REMARK 3 11 1.8600 - 1.8000 1.00 2169 144 0.1921 0.2056 REMARK 3 12 1.8000 - 1.7500 0.98 2114 139 0.2172 0.2653 REMARK 3 13 1.7500 - 1.7100 0.94 2001 133 0.2120 0.2553 REMARK 3 14 1.7100 - 1.6700 0.85 1841 122 0.2132 0.2555 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.020 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 : 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 8ZLZ 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_1300048014. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-24 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 : BL18U1 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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32268 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 58.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 22.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 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 (%): 42.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M TRIS REMARK 280 PH8.5, 1.26 M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291.15K 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 59.05400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.74650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.74650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.52700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.74650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.74650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 88.58100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.74650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.74650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.52700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.74650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.74650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 88.58100 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 59.05400 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D 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 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 75 -92.92 -115.91 REMARK 500 LYS A 100 56.39 37.32 REMARK 500 LYS A 123 45.00 -94.82 REMARK 500 ASP A 124 61.15 -119.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 8ZLZ A 13 142 UNP Q8YXC3 Q8YXC3_NOSS1 13 142 DBREF 8ZLZ B 13 142 UNP Q8YXC3 Q8YXC3_NOSS1 13 142 DBREF 8ZLZ D 1 15 PDB 8ZLZ 8ZLZ 1 15 SEQRES 1 A 130 SER LYS TRP ARG SER GLN LEU ASP ARG PHE VAL LYS GLU SEQRES 2 A 130 ASN GLN GLN ASP LEU ALA ALA LEU PHE TRP GLY LEU TRP SEQRES 3 A 130 LEU GLU ASN GLY ASP SER GLN GLY THR ILE GLY ILE ASP SEQRES 4 A 130 LEU GLN PRO THR PRO HIS PHE VAL TYR CYS PRO LYS ASP SEQRES 5 A 130 ALA VAL GLU LYS LEU ASN ASN ASN VAL GLU ASN ARG LEU SEQRES 6 A 130 GLN GLU LEU LEU GLY ILE ILE GLU HIS ASN GLN PRO GLU SEQRES 7 A 130 ILE GLU VAL LEU MET ILE GLY ILE GLY LYS GLY GLU ILE SEQRES 8 A 130 LYS LEU ILE GLN PHE ALA PRO GLU PRO PRO PRO PRO VAL SEQRES 9 A 130 CYS PHE GLU GLN VAL GLY LYS ASP ILE ASP GLY LEU LEU SEQRES 10 A 130 GLU LEU LEU GLU GLN ARG MET SER GLY GLU ILE VAL VAL SEQRES 1 B 130 SER LYS TRP ARG SER GLN LEU ASP ARG PHE VAL LYS GLU SEQRES 2 B 130 ASN GLN GLN ASP LEU ALA ALA LEU PHE TRP GLY LEU TRP SEQRES 3 B 130 LEU GLU ASN GLY ASP SER GLN GLY THR ILE GLY ILE ASP SEQRES 4 B 130 LEU GLN PRO THR PRO HIS PHE VAL TYR CYS PRO LYS ASP SEQRES 5 B 130 ALA VAL GLU LYS LEU ASN ASN ASN VAL GLU ASN ARG LEU SEQRES 6 B 130 GLN GLU LEU LEU GLY ILE ILE GLU HIS ASN GLN PRO GLU SEQRES 7 B 130 ILE GLU VAL LEU MET ILE GLY ILE GLY LYS GLY GLU ILE SEQRES 8 B 130 LYS LEU ILE GLN PHE ALA PRO GLU PRO PRO PRO PRO VAL SEQRES 9 B 130 CYS PHE GLU GLN VAL GLY LYS ASP ILE ASP GLY LEU LEU SEQRES 10 B 130 GLU LEU LEU GLU GLN ARG MET SER GLY GLU ILE VAL VAL SEQRES 1 D 15 PHE ARG GLU ASN VAL ASN ALA ILE ARG PRO PHE GLY ARG SEQRES 2 D 15 ARG PRO FORMUL 4 HOH *299(H2 O) HELIX 1 AA1 SER A 13 ASN A 26 1 14 HELIX 2 AA2 ASN A 26 GLY A 42 1 17 HELIX 3 AA3 PRO A 62 ASN A 72 1 11 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 ILE A 140 1 17 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 VAL B 73 1 12 HELIX 10 AB1 LEU B 77 ASN B 87 1 11 HELIX 11 AB2 PRO B 113 GLY B 122 1 10 HELIX 12 AB3 ASP B 124 SER B 137 1 14 HELIX 13 AB4 PHE D 1 VAL D 5 5 5 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 98 N ILE A 50 SHEET 4 AA1 4 GLU A 102 PHE A 108 -1 O LYS A 104 N GLY A 97 SHEET 1 AA2 5 ILE B 103 PHE B 108 0 SHEET 2 AA2 5 VAL B 93 ILE B 98 -1 N GLY B 97 O LYS B 104 SHEET 3 AA2 5 THR B 47 ASP B 51 1 N ILE B 50 O ILE B 98 SHEET 4 AA2 5 HIS B 57 CYS B 61 -1 O VAL B 59 N GLY B 49 SHEET 5 AA2 5 ASN D 6 ALA D 7 -1 O ASN D 6 N TYR B 60 CISPEP 1 GLN A 53 PRO A 54 0 -1.58 CISPEP 2 GLU A 111 PRO A 112 0 -0.08 CISPEP 3 GLN B 53 PRO B 54 0 -4.25 CISPEP 4 GLU B 111 PRO B 112 0 -2.94 CRYST1 67.493 67.493 118.108 90.00 90.00 90.00 P 41 21 2 16 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 0.014816 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014816 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008467 0.00000