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- PDB-6non: Structure of Cyanthece apo McdA -

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Basic information

Entry
Database: PDB / ID: 6non
TitleStructure of Cyanthece apo McdA
ComponentsCobyrinic acid ac-diamide synthase
KeywordsDNA BINDING PROTEIN / nonspecific DNA binding protein / Walker box / ParA-like / Carboxysome / McdA / McdB
Function / homology
Function and homology information


carbon fixation / nucleoid / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / hydrolase activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
: / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Maintenance of carboxysome distribution protein A
Similarity search - Component
Biological speciesCyanothece (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.68 Å
AuthorsSchumacher, M.A.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structures of maintenance of carboxysome distribution Walker-box McdA and McdB adaptor homologs.
Authors: Schumacher, M.A. / Henderson, M. / Zhang, H.
History
DepositionJan 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cobyrinic acid ac-diamide synthase
B: Cobyrinic acid ac-diamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1034
Polymers58,6512
Non-polymers4522
Water1,42379
1
A: Cobyrinic acid ac-diamide synthase


Theoretical massNumber of molelcules
Total (without water)29,3261
Polymers29,3261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cobyrinic acid ac-diamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7773
Polymers29,3261
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155.352, 155.352, 180.669
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Cobyrinic acid ac-diamide synthase / McdA


Mass: 29325.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece (bacteria) / Gene: PCC7424_5529 / Production host: Escherichia coli (E. coli) / References: UniProt: B7KMS4
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 5.39 Å3/Da / Density % sol: 77.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 2, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.68→134.5 Å / Num. obs: 61015 / % possible obs: 80.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 57.51 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.045 / Rsym value: 0.07 / Net I/σ(I): 17.6
Reflection shellResolution: 2.68→275 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.616 / Rpim(I) all: 0.47 / Rsym value: 0.567

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.68→77.676 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.02 / Phase error: 23.2
RfactorNum. reflection% reflection
Rfree0.2224 2843 4.66 %
Rwork0.1844 --
obs0.1862 61015 89.06 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 30.912 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7585 Å20 Å2-0 Å2
2--0.7585 Å20 Å2
3----4.2091 Å2
Refinement stepCycle: LAST / Resolution: 2.68→77.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 28 79 3949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093941
X-RAY DIFFRACTIONf_angle_d1.2945347
X-RAY DIFFRACTIONf_dihedral_angle_d15.6081455
X-RAY DIFFRACTIONf_chiral_restr0.076624
X-RAY DIFFRACTIONf_plane_restr0.007685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6801-2.77580.31271900.32863752X-RAY DIFFRACTION58
2.7758-2.8870.35912210.29624525X-RAY DIFFRACTION70
2.887-3.01840.28052850.27935750X-RAY DIFFRACTION88
3.0184-3.17750.30163130.26676360X-RAY DIFFRACTION97
3.1775-3.37660.2983180.23736346X-RAY DIFFRACTION97
3.3766-3.63730.24243110.20746347X-RAY DIFFRACTION97
3.6373-4.00330.2263050.1686320X-RAY DIFFRACTION97
4.0033-4.58260.18043020.13096295X-RAY DIFFRACTION96
4.5826-5.77330.15153010.12936244X-RAY DIFFRACTION96
5.7733-77.70860.19822970.17136233X-RAY DIFFRACTION95

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