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- PDB-9qlg: Crystal structure of the transcription factor MraZ from Mycoplasm... -

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Basic information

Entry
Database: PDB / ID: 9qlg
TitleCrystal structure of the transcription factor MraZ from Mycoplasma genitalium
ComponentsTranscriptional regulator MraZ
KeywordsTRANSCRIPTION / Transcription factor / octameric
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 / MraZ domain / MraZ, C-terminal / MraZ superfamily / MraZ protein, putative antitoxin-like / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily
Similarity search - Domain/homology
Transcriptional regulator MraZ
Similarity search - Component
Biological speciesMycoplasmoides genitalium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSanchez-Alba, L. / Reverter, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2021-124602OB-I00 Spain
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for transcriptional regulation by the cell division regulator MraZ in Mycoplasma genitalium
Authors: Sanchez-Alba, L. / Varejao, N. / Durand, A. / Garcia-Pardo, J. / Carreras-Caballe, M. / Amador, V. / Pinyol, J. / Reverter, D.
History
DepositionMar 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator MraZ
B: Transcriptional regulator MraZ
C: Transcriptional regulator MraZ
D: Transcriptional regulator MraZ


Theoretical massNumber of molelcules
Total (without water)73,9884
Polymers73,9884
Non-polymers00
Water8,179454
1
A: Transcriptional regulator MraZ
D: Transcriptional regulator MraZ

A: Transcriptional regulator MraZ
D: Transcriptional regulator MraZ

A: Transcriptional regulator MraZ
D: Transcriptional regulator MraZ

A: Transcriptional regulator MraZ
D: Transcriptional regulator MraZ


Theoretical massNumber of molelcules
Total (without water)147,9758
Polymers147,9758
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area22210 Å2
ΔGint-139 kcal/mol
Surface area46030 Å2
2
B: Transcriptional regulator MraZ
C: Transcriptional regulator MraZ

B: Transcriptional regulator MraZ
C: Transcriptional regulator MraZ

B: Transcriptional regulator MraZ
C: Transcriptional regulator MraZ

B: Transcriptional regulator MraZ
C: Transcriptional regulator MraZ


Theoretical massNumber of molelcules
Total (without water)147,9758
Polymers147,9758
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area23050 Å2
ΔGint-135 kcal/mol
Surface area48640 Å2
Unit cell
Length a, b, c (Å)143.100, 143.100, 71.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
Transcriptional regulator MraZ


Mass: 18496.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasmoides genitalium (bacteria) / Gene: mraZ, MG221 / Production host: Escherichia coli (E. coli) / References: UniProt: P47463
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2.0 M Ammonium sulfate 0.1 M Sodium cacodylate pH 6.5, 0.2 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.956→101.187 Å / Num. obs: 37663 / % possible obs: 87.3 % / Redundancy: 3.8 % / CC1/2: 0.774 / Net I/σ(I): 3.9
Reflection shellResolution: 1.956→2.119 Å / Num. unique obs: 1883 / CC1/2: 0.116

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→45.25 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 1840 4.89 %
Rwork0.1881 --
obs0.1909 37616 71.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4534 0 0 454 4988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074612
X-RAY DIFFRACTIONf_angle_d0.8556228
X-RAY DIFFRACTIONf_dihedral_angle_d6.091598
X-RAY DIFFRACTIONf_chiral_restr0.055706
X-RAY DIFFRACTIONf_plane_restr0.005812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.307450.1944126X-RAY DIFFRACTION3
2.01-2.050.2769410.2528503X-RAY DIFFRACTION17
2.07-2.130.2962860.23391637X-RAY DIFFRACTION44
2.13-2.210.3061430.22182525X-RAY DIFFRACTION67
2.21-2.30.30581230.2112629X-RAY DIFFRACTION69
2.3-2.40.29511570.21853272X-RAY DIFFRACTION86
2.4-2.530.25621950.21093391X-RAY DIFFRACTION90
2.53-2.690.27211740.21353065X-RAY DIFFRACTION80
2.69-2.90.25541970.193823X-RAY DIFFRACTION100
2.9-3.190.23911930.17943800X-RAY DIFFRACTION100
3.19-3.630.19891740.16143501X-RAY DIFFRACTION94
3.66-4.60.17361500.14463592X-RAY DIFFRACTION94
4.6-45.250.22082020.17663912X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -26.9781 Å / Origin y: 16.9461 Å / Origin z: -15.4401 Å
111213212223313233
T0.0136 Å20.0063 Å20.0205 Å2-0.0292 Å20.0137 Å2--0.0653 Å2
L0.1021 °20.0143 °2-0.0367 °2-0.1816 °2-0.0187 °2--0.281 °2
S0.0086 Å °-0.0076 Å °-0.0062 Å °0.0049 Å °0.0099 Å °0.048 Å °0.0382 Å °-0.0033 Å °-0.0121 Å °
Refinement TLS groupSelection details: all

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