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- PDB-5h3b: Crystal Structure of SeMet-BioG from Haemophilus influenzae at 1.... -

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Basic information

Entry
Database: PDB / ID: 5h3b
TitleCrystal Structure of SeMet-BioG from Haemophilus influenzae at 1.49 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 / ISOPROPYL ALCOHOL / Uncharacterized protein HI_1552
Function and homology information
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.492 Å
AuthorsShi, J. / Guo, Z.
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
DepositionOct 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,0394
Polymers52,8872
Non-polymers1522
Water8,467470
1
A: Uncharacterized protein HI_1552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5963
Polymers26,4431
Non-polymers1522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-1 kcal/mol
Surface area9420 Å2
MethodPISA
2
B: Uncharacterized protein HI_1552


Theoretical massNumber of molelcules
Total (without water)26,4431
Polymers26,4431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.154, 69.471, 72.034
Angle α, β, γ (deg.)90.000, 93.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein HI_1552


Mass: 26443.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Strain: KW20 / Gene: HI_1552 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P44251, carboxylesterase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10%(v/v) iso-propanol, 0.1M citric acid/sodium citrate pH 5.6, 22% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.49→32.45 Å / Num. obs: 70407 / % possible obs: 99.6 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Net I/av σ(I): 19.51 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.49-1.546.50.690.87196.38
1.54-1.617.30.570.931100
1.61-1.687.40.4280.9561100
1.68-1.777.40.3040.9771100
1.77-1.887.50.2130.9871100
1.88-2.027.50.1370.9941100
2.02-2.237.50.0980.9961100
2.23-2.557.50.0850.9961100
2.55-3.217.50.0840.9951100
3.21-32.457.40.0480.998199.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIX1.8.4_1496phasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.492→32.45 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.76
RfactorNum. reflection% reflection
Rfree0.1816 1954 2.84 %
Rwork0.1469 --
obs0.1479 68819 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.8 Å2 / Biso mean: 25.32 Å2 / Biso min: 8.42 Å2
Refinement stepCycle: final / Resolution: 1.492→32.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3474 0 10 470 3954
Biso mean--18.81 35.51 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073636
X-RAY DIFFRACTIONf_angle_d1.1264954
X-RAY DIFFRACTIONf_chiral_restr0.044523
X-RAY DIFFRACTIONf_plane_restr0.005630
X-RAY DIFFRACTIONf_dihedral_angle_d13.4271277
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 (%)
1.492-1.52930.31631220.22974245436787
1.5293-1.57070.25941290.20544607473694
1.5707-1.61690.2691340.17784665479996
1.6169-1.66910.22921510.16714675482696
1.6691-1.72880.19551240.15694767489197
1.7288-1.7980.20581510.14554795494698
1.798-1.87980.19741380.13944782492098
1.8798-1.97890.17131460.12564807495399
1.9789-2.10280.17631450.1284909505499
2.1028-2.26520.15691410.127748615002100
2.2652-2.4930.19271330.136649295062100
2.493-2.85360.15881520.154448925044100
2.8536-3.59450.17941440.148549365080100
3.5945-32.45770.16061440.143949955139100

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