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- PDB-6mr1: RbcS-like subdomain of CcmM -

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Basic information

Entry
Database: PDB / ID: 6mr1
TitleRbcS-like subdomain of CcmM
ComponentsCarbon dioxide concentrating mechanism protein
KeywordsPROTEIN BINDING / carboxysome / RubisCO / CcmM
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Carboxysome assembly protein CcmM / : / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
: / THIOCYANATE ION / Carboxysome assembly protein CcmM
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsRyan, P. / Kimber, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04045-2015 Canada
CitationJournal: J. Biol. Chem. / Year: 2019
Title: The small RbcS-like domains of the beta-carboxysome structural protein CcmM bind RubisCO at a site distinct from that binding the RbcS subunit.
Authors: Ryan, P. / Forrester, T.J.B. / Wroblewski, C. / Kenney, T.M.G. / Kitova, E.N. / Klassen, J.S. / Kimber, M.S.
History
DepositionOct 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 6, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbon dioxide concentrating mechanism protein
B: Carbon dioxide concentrating mechanism protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,19910
Polymers21,6782
Non-polymers5218
Water3,585199
1
A: Carbon dioxide concentrating mechanism protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0304
Polymers10,8391
Non-polymers1903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbon dioxide concentrating mechanism protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1696
Polymers10,8391
Non-polymers3305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.900, 73.560, 76.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carbon dioxide concentrating mechanism protein


Mass: 10839.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: ccmM / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8DKB5

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Non-polymers , 5 types, 207 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.48 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.8 M ammonium sulfate, 0.2 M sodium thiocyanate, 10 mM CoCl2, 0.1 M MES pH 6.5, 30 mg/mL protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 36148 / % possible obs: 98.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.3
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2559 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→38.285 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.28
RfactorNum. reflection% reflection
Rfree0.1946 1808 5 %
Rwork0.1714 --
obs0.1726 36146 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→38.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 20 199 1627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171667
X-RAY DIFFRACTIONf_angle_d1.5932292
X-RAY DIFFRACTIONf_dihedral_angle_d26.642700
X-RAY DIFFRACTIONf_chiral_restr0.103247
X-RAY DIFFRACTIONf_plane_restr0.009304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.38650.27431330.25462526X-RAY DIFFRACTION95
1.3865-1.42730.26711340.22372538X-RAY DIFFRACTION97
1.4273-1.47340.25941360.20992599X-RAY DIFFRACTION98
1.4734-1.5260.20491360.19692568X-RAY DIFFRACTION97
1.526-1.58710.22411380.19312624X-RAY DIFFRACTION99
1.5871-1.65940.18021370.18032598X-RAY DIFFRACTION98
1.6594-1.74690.21611380.18122629X-RAY DIFFRACTION99
1.7469-1.85630.21461380.16982622X-RAY DIFFRACTION99
1.8563-1.99960.19351400.16872667X-RAY DIFFRACTION99
1.9996-2.20080.18761410.15932678X-RAY DIFFRACTION99
2.2008-2.51920.19391410.15782682X-RAY DIFFRACTION99
2.5192-3.17370.18571450.17372739X-RAY DIFFRACTION100
3.1737-38.30040.18051510.16262868X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.6696-0.07461.25832.19861.04985.4044-0.0826-0.11080.49960.2236-0.0476-0.4108-0.32480.12560.12910.1306-0.00140.01930.2217-0.01550.153219.136124.070550.5921
25.58751.29711.68618.07441.3435.51850.1901-0.3617-0.40140.5155-0.12020.21950.3444-0.56-0.08570.1324-0.05460.00180.20430.05750.10128.782512.967251.1529
37.9406-3.9573-0.96575.42731.25922.1249-0.002-0.12820.0997-0.00810.0064-0.1596-0.1893-0.01060.00890.1153-0.01320.00360.09570.01260.060518.537419.12345.1352
46.48494.2647-3.84054.0008-4.59366.6510.2729-0.04540.34740.6273-0.09840.0853-0.4261-0.048-0.09110.16860.01870.01940.16560.01950.14943.4246-12.205235.0658
53.81341.9282-0.93655.8939-0.81382.09630.0025-0.0493-0.425-0.0499-0.204-0.88670.24050.14620.15620.13820.0099-0.00870.14740.02710.142911.2157-24.172428.7539
66.8139-4.35332.49914.8271-4.70397.63910.11590.36110.0377-0.2616-0.2414-0.4925-0.1114-0.110.12020.1746-0.01940.03840.2043-0.01160.190810.4568-18.955424.6766
73.9106-0.5720.51168.37662.95793.96850.03150.09570.1767-0.2269-0.05890.0049-0.0755-0.11310.0060.1114-0.01040.00050.17810.02150.10960.3254-15.965124.8276
85.8030.9542-0.0422.6507-0.13683.06340.00470.08210.1122-0.0228-0.0314-0.03250.17860.1582-0.00520.1260.023-0.00670.11370.01550.065611.4988-19.22731.7064
93.1465-1.26490.69126.88160.76821.81420.15010.0332-0.3071-0.3187-0.02940.25680.0749-0.1164-0.13530.1048-0.01830.0140.13710.03930.076414.047513.375943.3121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 252 through 271 )
2X-RAY DIFFRACTION2chain 'A' and (resid 272 through 285 )
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 313 )
4X-RAY DIFFRACTION4chain 'B' and (resid 227 through 241 )
5X-RAY DIFFRACTION5chain 'B' and (resid 242 through 257 )
6X-RAY DIFFRACTION6chain 'B' and (resid 258 through 271 )
7X-RAY DIFFRACTION7chain 'B' and (resid 272 through 286 )
8X-RAY DIFFRACTION8chain 'B' and (resid 287 through 312 )
9X-RAY DIFFRACTION9chain 'A' and (resid 226 through 251 )

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