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- PDB-5gng: Crystal Structure of BioG from Haemophilus influenzae at 1.26 Ang... -

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Basic information

Entry
Database: PDB / ID: 5gng
TitleCrystal Structure of BioG from Haemophilus influenzae at 1.26 Angstroms resolution
ComponentsUncharacterized protein HI_1552
KeywordsHYDROLASE / alpha/beta-hydrolase fold / pimeloyl-ACP methyl esterase / biotin biosynthesis
Function / homologyPimeloyl-ACP methyl esterase BioG / Pimeloyl-ACP methyl esterase BioG / Uncharacterized protein HI_1552
Function and homology information
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.26 Å
AuthorsShi, J. / Guo, Z.
Funding support Hong Kong, 2items
OrganizationGrant numberCountry
Research Grants CouncilGRF601413 Hong Kong
Research Grants CouncilN_HKUST621/1 Hong Kong
CitationJournal: Biochemistry / Year: 2016
Title: An Atypical alpha / beta-Hydrolase Fold Revealed in the Crystal Structure of Pimeloyl-Acyl Carrier Protein Methyl Esterase BioG from Haemophilus influenzae
Authors: Shi, J. / Cao, X. / Chen, Y. / Cronan, J.E. / Guo, Z.
History
DepositionJul 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein HI_1552
B: Uncharacterized protein HI_1552


Theoretical massNumber of molelcules
Total (without water)52,6052
Polymers52,6052
Non-polymers00
Water12,989721
1
A: Uncharacterized protein HI_1552


Theoretical massNumber of molelcules
Total (without water)26,3031
Polymers26,3031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein HI_1552


Theoretical massNumber of molelcules
Total (without water)26,3031
Polymers26,3031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.950, 67.830, 67.990
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein HI_1552


Mass: 26302.740 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: HI_1552 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P44251
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.01 Å3/Da / Density % sol: 38.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M magnesium acetate, 0.1M sodium cacodylate, 25% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: -h,k,l / Fraction: 0.46
ReflectionResolution: 1.26→30.392 Å / Num. obs: 105669 / % possible obs: 94.3 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.2
Reflection shellResolution: 1.26→1.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.622 / CC1/2: 0.673 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Blu-Icedata collection
Aimlessdata scaling
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHENIX1.8.4_1496phasing
RefinementResolution: 1.26→30.392 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.88
RfactorNum. reflection% reflection
Rfree0.1809 2088 1.98 %
Rwork0.1446 --
obs0.1483 105604 93.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.1 Å2 / Biso mean: 14.54 Å2 / Biso min: 6.56 Å2
Refinement stepCycle: final / Resolution: 1.26→30.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3523 0 0 721 4244
Biso mean---23.92 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063673
X-RAY DIFFRACTIONf_angle_d0.8725006
X-RAY DIFFRACTIONf_chiral_restr0.035524
X-RAY DIFFRACTIONf_plane_restr0.004641
X-RAY DIFFRACTIONf_dihedral_angle_d14.2721306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2602-1.29170.36631450.2787080722589
1.2917-1.32660.28051390.24327115725489
1.3266-1.36570.27491390.23437155729489
1.3657-1.40980.19911380.22047175731390
1.4098-1.46010.22741280.20277259738791
1.4601-1.51860.22821420.21497315745791
1.5186-1.58770.2181380.1777368750692
1.5877-1.67140.20231400.16697408754893
1.6714-1.77610.15911440.16797531767594
1.7761-1.91320.17111560.16027565772194
1.9132-2.10570.17421430.15687622776595
2.1057-2.41030.18571460.14457643778995
2.4103-3.03630.19591360.12347409754592
3.0363-30.40060.14311520.09557920807297

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