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- PDB-1xq4: Crystal Structure of the Putative ApaA Protein from Bordetella pe... -

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Basic information

Entry
Database: PDB / ID: 1xq4
TitleCrystal Structure of the Putative ApaA Protein from Bordetella pertussis, Northeast Structural Genomics Target BeR40
ComponentsProtein apaG
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / all beta protein / Protein Structure Initiative / PSI / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


: / Uncharacterised protein family ApaG / ApaG domain / ApaG domain / ApaG domain superfamily / ApaG domain / ApaG domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Protein ApaG
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsForouhar, F. / Yong, W. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Putative ApaA Protein from Bordetella pertussis, Northeast Structural Genomics Target BeR40
Authors: Forouhar, F. / Yong, W. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionOct 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein apaG
B: Protein apaG
C: Protein apaG
D: Protein apaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5348
Polymers63,1544
Non-polymers3804
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.559, 100.256, 108.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailspossibly tetramer

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Components

#1: Protein
Protein apaG


Mass: 15788.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: apaG / Plasmid: pET21(BL21) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7VU61
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.64 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mM Tris (pH 7.5), 14% PEG 8k, 50 mM KH2PO4, 25 mM Glycine, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97878 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 30, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97878 Å / Relative weight: 1
ReflectionResolution: 2.7→29.73 Å / Num. all: 55448 / Num. obs: 44550 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.072 / Net I/σ(I): 14.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.169 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→29.73 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 170845.38 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 4095 10 %RANDOM
Rwork0.241 ---
obs0.241 40779 90.1 %-
all-44550 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9627 Å2 / ksol: 0.316676 e/Å3
Displacement parametersBiso mean: 34 Å2
Baniso -1Baniso -2Baniso -3
1-7.58 Å20 Å20 Å2
2--1.96 Å20 Å2
3----9.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 20 306 4122
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_d27.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
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: 2.7→2.87 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 553 9.7 %
Rwork0.282 5161 -
obs--76 %

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