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- PDB-4czm: C. crescentus MreB, monomeric, AMPPNP -

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Basic information

Entry
Database: PDB / ID: 4czm
TitleC. crescentus MreB, monomeric, AMPPNP
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Cell shape-determining protein MreB / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesCAULOBACTER VIBRIOIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLowe, J. / van den Ent, 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 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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.value / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,8486
Polymers73,7872
Non-polymers1,0614
Water77543
1
A: ROD SHAPE-DETERMINING PROTEIN MREB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4243
Polymers36,8941
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ROD SHAPE-DETERMINING PROTEIN MREB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4243
Polymers36,8941
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.791, 67.791, 320.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-2014-

HOH

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Components

#1: Protein ROD SHAPE-DETERMINING PROTEIN MREB / MREB


Mass: 36893.504 Da / Num. of mol.: 2 / Fragment: RESIDUES 9-347 / Mutation: YES
Source method: isolated from a genetically manipulated source
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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.5 Å3/Da / Density % sol: 50.71 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97957
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 39419 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 60.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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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: 2.2→41.138 Å / SU ML: 0.39 / σ(F): 1.21 / Phase error: 30.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2766 3590 5 %
Rwork0.2087 --
obs0.212 39329 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→41.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 64 43 5065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0185086
X-RAY DIFFRACTIONf_angle_d1.8936888
X-RAY DIFFRACTIONf_dihedral_angle_d18.3681924
X-RAY DIFFRACTIONf_chiral_restr0.095810
X-RAY DIFFRACTIONf_plane_restr0.009894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.22890.32581560.31132659X-RAY DIFFRACTION100
2.2289-2.25950.41521460.33992651X-RAY DIFFRACTION100
2.2595-2.29180.41421810.34912571X-RAY DIFFRACTION100
2.2918-2.3260.36811420.32292662X-RAY DIFFRACTION100
2.326-2.36230.35141420.32552588X-RAY DIFFRACTION100
2.3623-2.4010.36171470.30372655X-RAY DIFFRACTION100
2.401-2.44240.37841150.28742702X-RAY DIFFRACTION100
2.4424-2.48680.36751290.26532643X-RAY DIFFRACTION100
2.4868-2.53470.30561140.26712682X-RAY DIFFRACTION100
2.5347-2.58640.39491250.27112658X-RAY DIFFRACTION100
2.5864-2.64260.38291290.2552633X-RAY DIFFRACTION100
2.6426-2.70410.34141160.26152704X-RAY DIFFRACTION100
2.7041-2.77170.36531410.26152597X-RAY DIFFRACTION100
2.7717-2.84660.38361210.25512678X-RAY DIFFRACTION100
2.8466-2.93030.32251320.2612682X-RAY DIFFRACTION100
2.9303-3.02490.34781440.25552621X-RAY DIFFRACTION100
3.0249-3.1330.33931130.25092648X-RAY DIFFRACTION100
3.133-3.25840.32471590.23832639X-RAY DIFFRACTION100
3.2584-3.40660.30361460.23652665X-RAY DIFFRACTION100
3.4066-3.58610.29131500.22592637X-RAY DIFFRACTION100
3.5861-3.81060.2981800.19452606X-RAY DIFFRACTION100
3.8106-4.10460.23091240.19142637X-RAY DIFFRACTION100
4.1046-4.51720.191460.15522666X-RAY DIFFRACTION100
4.5172-5.16980.24511400.16632626X-RAY DIFFRACTION100
5.1698-6.50920.29411370.19232648X-RAY DIFFRACTION100
6.5092-41.1450.19231150.16682665X-RAY DIFFRACTION99

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