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- PDB-2hql: Crystal structure of a small single-stranded DNA binding protein ... -

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Basic information

Entry
Database: PDB / ID: 2hql
TitleCrystal structure of a small single-stranded DNA binding protein from Mycoplasma pneumoniae
ComponentsHypothetical protein MG376 homolog
KeywordsDNA BINDING PROTEIN / Structural genomics / conserved hypothetical protein / Mycoplasma pneumoniae / GI:1673959 / MPN554 / MG376 / OB fold / Single-stranded DNA binding protein / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homologyProtein of unknown function DUF3217 / Protein of unknown function (DUF3217) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta / Uncharacterized protein MG376 homolog
Function and homology information
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsDas, D. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of a novel single-stranded DNA binding protein from Mycoplasma pneumoniae.
Authors: Das, D. / Hyun, H. / Lou, Y. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionJul 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 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: Hypothetical protein MG376 homolog
B: Hypothetical protein MG376 homolog
C: Hypothetical protein MG376 homolog
D: Hypothetical protein MG376 homolog
E: Hypothetical protein MG376 homolog
F: Hypothetical protein MG376 homolog


Theoretical massNumber of molelcules
Total (without water)76,9796
Polymers76,9796
Non-polymers00
Water3,027168
1
A: Hypothetical protein MG376 homolog
E: Hypothetical protein MG376 homolog


Theoretical massNumber of molelcules
Total (without water)25,6602
Polymers25,6602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-18 kcal/mol
Surface area12680 Å2
MethodPISA
2
B: Hypothetical protein MG376 homolog
C: Hypothetical protein MG376 homolog


Theoretical massNumber of molelcules
Total (without water)25,6602
Polymers25,6602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-14 kcal/mol
Surface area12140 Å2
MethodPISA
3
D: Hypothetical protein MG376 homolog
F: Hypothetical protein MG376 homolog


Theoretical massNumber of molelcules
Total (without water)25,6602
Polymers25,6602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-10 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.134, 103.134, 63.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Hypothetical protein MG376 homolog / G12_orf104 / Single-stranded DNA-binding protein


Mass: 12829.871 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Gene: MPN554, MP288 / Plasmid: pET21a derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21, B834 / References: UniProt: P75224
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / pH: 5.5
Details: 0.2M Ammonium Sulfate, 0.1M Bis-Tris pH 5.5, 25% w/v PEG 3350 (Index Screen 66), VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.50

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99186
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 23, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99186 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 51433 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.064 / Net I/σ(I): 13.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.304 / % possible all: 87.7

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.272 4382 8.5 %RANDOM
Rwork0.21 ---
obs0.21 46511 90.6 %-
all-48673 --
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å2-1 Å20 Å2
2---1.43 Å20 Å2
3---2.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5016 0 0 168 5184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Total num. of bins used: 6

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