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- PDB-6noo: Structure of Cyanothece McdA-AMPPNP complex -

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Basic information

Entry
Database: PDB / ID: 6noo
TitleStructure of Cyanothece McdA-AMPPNP complex
ComponentsMaintenance of carboxysome positioning A protein, MCDA
KeywordsDNA BINDING PROTEIN / McdA / McdB / carboxysome / ParA-like / Walker A
Function / homologyAAA domain / AAA domain / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-5'-TRIPHOSPHATE / Maintenance of carboxysome distribution protein A
Function and homology information
Biological speciesCyanothece (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maintenance of carboxysome positioning A protein, MCDA
B: Maintenance of carboxysome positioning A protein, MCDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3624
Polymers59,8312
Non-polymers5312
Water63135
1
A: Maintenance of carboxysome positioning A protein, MCDA


Theoretical massNumber of molelcules
Total (without water)29,9151
Polymers29,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maintenance of carboxysome positioning A protein, MCDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4473
Polymers29,9151
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.891, 154.891, 181.299
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Maintenance of carboxysome positioning A protein, MCDA


Mass: 29915.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: B7KMS4*PLUS
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, 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 / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 5.25 Å3/Da / Density % sol: 76.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.2 M sodium thiocyanate, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→134.14 Å / Num. obs: 81993 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 6.1 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rsym value: 0.061 / Net I/σ(I): 20.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1 / Num. unique all: 6986 / CC1/2: 0.356 / Rpim(I) all: 0.75 / Rsym value: 1.28 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NON

6non


Resolution: 2.5→134.14 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0.87 / Phase error: 24.3
RfactorNum. reflection% reflection
Rfree0.2248 3703 4.52 %
Rwork0.1973 --
obs0.1986 81993 97.36 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 54.034 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 253.51 Å2 / Biso mean: 73.61 Å2 / Biso min: 38.09 Å2
Baniso -1Baniso -2Baniso -3
1-2.3705 Å2-0 Å2-0 Å2
2--2.3705 Å20 Å2
3----4.7411 Å2
Refinement stepCycle: final / Resolution: 2.5→134.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 32 35 3965
Biso mean--82.78 66.44 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084003
X-RAY DIFFRACTIONf_angle_d1.1685432
X-RAY DIFFRACTIONf_chiral_restr0.072632
X-RAY DIFFRACTIONf_plane_restr0.004695
X-RAY DIFFRACTIONf_dihedral_angle_d16.0181481
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.58940.37613150.3646671698683
2.5894-2.69310.38013530.3487424777793
2.6931-2.81570.36423730.31987955832899
2.8157-2.96410.32513890.269980078396100
2.9641-3.14990.28573740.233480358409100
3.1499-3.39310.23313840.198980398423100
3.3931-3.73460.19213840.173980268410100
3.7346-4.2750.19153830.157580318414100
4.275-5.38610.17953710.146580578428100
5.3861-134.3330.21463770.207580458422100
Refinement TLS params.Method: refined / Origin x: -1.5084 Å / Origin y: -63.6188 Å / Origin z: -26.1516 Å
111213212223313233
T0.274 Å2-0.087 Å2-0.0113 Å2-0.6281 Å20.0041 Å2--0.4291 Å2
L0.9804 °2-0.2418 °2-1.2131 °2-0.1783 °20.0591 °2--1.3659 °2
S-0.1404 Å °0.0222 Å °-0.0693 Å °-0.0294 Å °0.0662 Å °0.0101 Å °-0.0424 Å °-0.0758 Å °-0.0006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-7 - 251
2X-RAY DIFFRACTION1allB-7 - 251
3X-RAY DIFFRACTION1allF501
4X-RAY DIFFRACTION1allG4
5X-RAY DIFFRACTION1allS1 - 35

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