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- PDB-4czf: C. crescentus MreB, single filament, ADP -

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Basic information

Entry
Database: PDB / ID: 4czf
TitleC. crescentus MreB, single filament, ADP
ComponentsROD SHAPE-DETERMINING PROTEIN MREB
KeywordsSTRUCTURAL PROTEIN / BACTERIAL ACTIN / BACTERIAL CYTOSKELETON
Function / homology
Function and homology information


cell morphogenesis / regulation of cell shape / ATP binding / cytoplasm
Similarity search - Function
Cell shape determining protein MreB / : / MreB/Mbl protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cell shape-determining protein MreB / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesCAULOBACTER VIBRIOIDES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsLowe, J. / vandenEnt, F.
CitationJournal: Elife / Year: 2014
Title: Bacterial Actin Mreb Forms Antiparallel Double Filaments.
Authors: Van Den Ent, F. / Izore, T. / Bharat, T.A. / Johnson, C.M. / Lowe, J.
History
DepositionApr 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Atomic model / Database references / Other
Revision 1.2Jul 2, 2014Group: Atomic model
Revision 1.3Aug 6, 2014Group: Other
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ROD SHAPE-DETERMINING PROTEIN MREB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3173
Polymers36,8651
Non-polymers4522
Water7,873437
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.548, 71.815, 53.731
Angle α, β, γ (deg.)90.00, 100.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ROD SHAPE-DETERMINING PROTEIN MREB


Mass: 36865.496 Da / Num. of mol.: 1 / Fragment: RESIDUES 9-347 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: M-I9-CCMREB(F102S, V103G)-A347-GSHHHHHH / Source: (gene. exp.) CAULOBACTER VIBRIOIDES (bacteria) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: B8H609, UniProt: A0A0H3C7V4*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.65 Å3/Da / Density % sol: 53.65 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: MARESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 46866 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 42.1
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 10.7 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JCE

1jce


Resolution: 1.64→21.406 Å / SU ML: 0.4 / σ(F): 1.46 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 4566 5 %
Rwork0.1725 --
obs0.1736 46866 98.46 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.882 Å2 / ksol: 0.461 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3593 Å20 Å2-2.0623 Å2
2--1.1045 Å20 Å2
3---1.2547 Å2
Refinement stepCycle: LAST / Resolution: 1.64→21.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 28 437 2897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172490
X-RAY DIFFRACTIONf_angle_d1.633369
X-RAY DIFFRACTIONf_dihedral_angle_d13.98943
X-RAY DIFFRACTIONf_chiral_restr0.114399
X-RAY DIFFRACTIONf_plane_restr0.008434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6402-1.65880.29871310.22112533X-RAY DIFFRACTION87
1.6588-1.67830.31081540.22212907X-RAY DIFFRACTION100
1.6783-1.69880.26341560.20422957X-RAY DIFFRACTION99
1.6988-1.72030.2251480.19712994X-RAY DIFFRACTION100
1.7203-1.74290.22661410.18972900X-RAY DIFFRACTION100
1.7429-1.76680.2421690.18882898X-RAY DIFFRACTION100
1.7668-1.7920.28161470.19252993X-RAY DIFFRACTION100
1.792-1.81870.23911260.18872917X-RAY DIFFRACTION100
1.8187-1.84710.27411860.1972899X-RAY DIFFRACTION100
1.8471-1.87740.2531510.2022935X-RAY DIFFRACTION99
1.8774-1.90970.22871730.21642715X-RAY DIFFRACTION93
1.9097-1.94440.26011290.22512922X-RAY DIFFRACTION100
1.9444-1.98180.20241690.18812959X-RAY DIFFRACTION99
1.9818-2.02220.21371450.17292887X-RAY DIFFRACTION100
2.0222-2.06620.19261430.17152978X-RAY DIFFRACTION100
2.0662-2.11420.21781560.16642951X-RAY DIFFRACTION100
2.1142-2.1670.18941480.16782919X-RAY DIFFRACTION100
2.167-2.22560.19531540.17662840X-RAY DIFFRACTION96
2.2256-2.2910.20991520.18862862X-RAY DIFFRACTION98
2.291-2.36480.20311690.16642870X-RAY DIFFRACTION98
2.3648-2.44920.1711810.15182926X-RAY DIFFRACTION100
2.4492-2.54710.1831840.15462877X-RAY DIFFRACTION100
2.5471-2.66290.16761650.15282963X-RAY DIFFRACTION100
2.6629-2.8030.16291780.15772911X-RAY DIFFRACTION100
2.803-2.97820.19921530.16132943X-RAY DIFFRACTION100
2.9782-3.20740.1611240.16442976X-RAY DIFFRACTION100
3.2074-3.52890.17881380.15622922X-RAY DIFFRACTION100
3.5289-4.03660.16811450.16182939X-RAY DIFFRACTION99
4.0366-5.07440.14791350.15062867X-RAY DIFFRACTION97
5.0744-21.40830.23161160.20282659X-RAY DIFFRACTION89

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