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- PDB-4czl: C. crescentus MreB, monomeric, ADP -

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Basic information

Entry
Database: PDB / ID: 4czl
TitleC. crescentus MreB, monomeric, 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,3453
Polymers36,8941
Non-polymers4522
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.651, 68.651, 68.731
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 36893.504 Da / Num. of mol.: 1 / 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.: 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.: 207 / 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: 2.53 Å3/Da / Density % sol: 51.47 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / 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: 1.6→50 Å / Num. obs: 47159 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.7 / % possible all: 98.4

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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: 1.6→44.965 Å / SU ML: 0.22 / σ(F): 0.4 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 4166 5 %
Rwork0.2001 --
obs0.2014 47159 87.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→44.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 28 207 2691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072513
X-RAY DIFFRACTIONf_angle_d1.3083401
X-RAY DIFFRACTIONf_dihedral_angle_d17.141951
X-RAY DIFFRACTIONf_chiral_restr0.082403
X-RAY DIFFRACTIONf_plane_restr0.005440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.37271180.34792593X-RAY DIFFRACTION84
1.6182-1.63720.39351520.34662569X-RAY DIFFRACTION87
1.6372-1.65720.37131300.3342568X-RAY DIFFRACTION87
1.6572-1.67820.34721290.31032644X-RAY DIFFRACTION87
1.6782-1.70020.33891250.3062630X-RAY DIFFRACTION86
1.7002-1.72350.31311160.29992471X-RAY DIFFRACTION82
1.7235-1.74820.31381560.29522625X-RAY DIFFRACTION86
1.7482-1.77430.35171540.28472614X-RAY DIFFRACTION89
1.7743-1.8020.28331170.27422760X-RAY DIFFRACTION88
1.802-1.83150.28271480.25852701X-RAY DIFFRACTION88
1.8315-1.86310.2461400.23732645X-RAY DIFFRACTION89
1.8631-1.8970.2571310.22842705X-RAY DIFFRACTION90
1.897-1.93350.26191600.23362647X-RAY DIFFRACTION89
1.9335-1.97290.27061240.23572700X-RAY DIFFRACTION88
1.9729-2.01580.26561170.23342740X-RAY DIFFRACTION87
2.0158-2.06270.27321340.22372454X-RAY DIFFRACTION83
2.0627-2.11430.28321360.23782747X-RAY DIFFRACTION90
2.1143-2.17150.25531390.2192681X-RAY DIFFRACTION89
2.1715-2.23540.25791440.20812638X-RAY DIFFRACTION88
2.2354-2.30750.25011280.20782730X-RAY DIFFRACTION90
2.3075-2.390.2091390.20392781X-RAY DIFFRACTION91
2.39-2.48570.25241770.20312649X-RAY DIFFRACTION89
2.4857-2.59880.24711350.20782586X-RAY DIFFRACTION85
2.5988-2.73580.22571250.20622683X-RAY DIFFRACTION89
2.7358-2.90720.20171450.19572639X-RAY DIFFRACTION88
2.9072-3.13160.21761600.19552864X-RAY DIFFRACTION91
3.1316-3.44660.21781650.1892681X-RAY DIFFRACTION91
3.4466-3.94510.22621570.17082588X-RAY DIFFRACTION87
3.9451-4.96940.17751200.15642751X-RAY DIFFRACTION90
4.9694-44.98280.16981450.18222742X-RAY DIFFRACTION91

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