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- PDB-1n0f: CRYSTAL STRUCTURE OF A CELL DIVISION AND CELL WALL BIOSYNTHESIS P... -

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Basic information

Entry
Database: PDB / ID: 1n0f
TitleCRYSTAL STRUCTURE OF A CELL DIVISION AND CELL WALL BIOSYNTHESIS PROTEIN UPF0040 FROM MYCOPLASMA PNEUMONIAE: INDICATION OF A NOVEL FOLD WITH A POSSIBLE NEW CONSERVED SEQUENCE MOTIF
ComponentsProtein mraZ
KeywordsBIOSYNTHETIC PROTEIN / Cell Division / cell wall biosynthesis protein / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


negative regulation of DNA-templated transcription initiation / nucleoid / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cytoplasm
Similarity search - Function
Transcriptional regulator MraZ domain / Transcriptional regulator MraZ / MraZ domain / MraZ, C-terminal / MraZ superfamily / MraZ protein, putative antitoxin-like / Chemotaxis protein chec / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily ...Transcriptional regulator MraZ domain / Transcriptional regulator MraZ / MraZ domain / MraZ, C-terminal / MraZ superfamily / MraZ protein, putative antitoxin-like / Chemotaxis protein chec / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator MraZ
Similarity search - Component
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsChen, S. / Jancrick, J. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): a novel fold with a conserved sequence motif.
Authors: Chen, S. / Jancrick, J. / Yokota, H. / Kim, R. / Kim, S.-H.
History
DepositionOct 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein mraZ
B: Protein mraZ
C: Protein mraZ
D: Protein mraZ
E: Protein mraZ
F: Protein mraZ
G: Protein mraZ
H: Protein mraZ


Theoretical massNumber of molelcules
Total (without water)154,7438
Polymers154,7438
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22310 Å2
ΔGint-137 kcal/mol
Surface area44900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.893, 101.180, 169.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is an octamer ring structure.

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Components

#1: Protein
Protein mraZ / UPF0040 Pfam protein


Mass: 19342.865 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Production host: Escherichia coli (E. coli) / References: UniProt: P75467
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
119 mg/mlprotein1drop
20.2 Mmagnesium acetate1drop
320 %(w/v)PEG33501drop
410 %glycerol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 13, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 36610 / Num. obs: 36274 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 55.5 Å2 / Rsym value: 0.096 / Net I/σ(I): 12.8
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.326 / % possible all: 99
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % possible obs: 99.3 % / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 99.6 % / Num. unique obs: 1796 / Rmerge(I) obs: 0.326

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.8→13.01 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2142024.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1786 5.1 %RANDOM
Rwork0.24 ---
all0.24 36610 --
obs0.24 35271 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.0047 Å2 / ksol: 0.335115 e/Å3
Displacement parametersBiso mean: 48.2 Å2
Baniso -1Baniso -2Baniso -3
1-17.1 Å20 Å20 Å2
2---18.03 Å20 Å2
3---0.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→13.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8984 0 0 184 9168
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.882.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 291 5 %
Rwork0.327 5510 -
obs--96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02

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