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- PDB-6kxr: Crystal structure of wild type Alp1U from the biosynthesis of kin... -

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Basic information

Entry
Database: PDB / ID: 6kxr
TitleCrystal structure of wild type Alp1U from the biosynthesis of kinamycins
ComponentsPutative hydrolase
KeywordsHYDROLASE / Hydrolyse epoxide / Cis-vicinal diol
Function / homology
Function and homology information


Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
D-MALATE / Putative hydrolase / Putative hydrolase
Similarity search - Component
Biological speciesStreptomyces ambofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45073679781 Å
AuthorsZhang, L. / Yingli, Z. / De, B.C. / Zhang, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China41606193 China
National Natural Science Foundation of China31820103003 China
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Mutation of an atypical oxirane oxyanion hole improves regioselectivity of the alpha / beta-fold epoxide hydrolase Alp1U.
Authors: Zhang, L. / De, B.C. / Zhang, W. / Mandi, A. / Fang, Z. / Yang, C. / Zhu, Y. / Kurtan, T. / Zhang, C.
History
DepositionSep 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: Putative hydrolase
B: Putative hydrolase
C: Putative hydrolase
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3385
Polymers148,2044
Non-polymers1341
Water2,288127
1
A: Putative hydrolase
D: Putative hydrolase


Theoretical massNumber of molelcules
Total (without water)74,1022
Polymers74,1022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-20 kcal/mol
Surface area21310 Å2
MethodPISA
2
B: Putative hydrolase
C: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2363
Polymers74,1022
Non-polymers1341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-22 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.09, 101.58, 117.42
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Putative hydrolase / epoxy hydrolase Alp1U


Mass: 37050.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ambofaciens (strain ATCC 23877 / 3486 / DSM 40053 / JCM 4204 / NBRC 12836 / NRRL B-2516) (bacteria)
Gene: SAMT0137, SAMT0138 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q1RQU8, UniProt: A0A0K2AJY3*PLUS, epoxide hydrolase
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.95 Å3/Da / Density % sol: 37.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M MMT PH5.0, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97894 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 2.45073679781→70.19 Å / Num. obs: 43063 / % possible obs: 99.35 % / Redundancy: 2 % / Biso Wilson estimate: 46.6816931705 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.02819 / Net I/σ(I): 13.73
Reflection shellResolution: 2.451→2.538 Å / Rmerge(I) obs: 0.2004 / Num. unique obs: 4255 / CC1/2: 0.846

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
PHENIX1.9_1692+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45073679781→70.1866527268 Å / SU ML: 0.339490266101 / Cross valid method: FREE R-VALUE / σ(F): 1.3435988873 / Phase error: 24.1668710666
RfactorNum. reflection% reflection
Rfree0.234445837871 2052 4.76621838199 %
Rwork0.168676881612 --
obs0.171747585964 43053 99.3377941855 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.2833727776 Å2
Refinement stepCycle: LAST / Resolution: 2.45073679781→70.1866527268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9097 0 9 127 9233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008184038640999365
X-RAY DIFFRACTIONf_angle_d1.1091975783712747
X-RAY DIFFRACTIONf_chiral_restr0.04312293125631337
X-RAY DIFFRACTIONf_plane_restr0.005088843414341678
X-RAY DIFFRACTIONf_dihedral_angle_d14.56676825243342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45073679781-2.50770.3099316812471230.2189417208212711X-RAY DIFFRACTION99.5433789954
2.5077-2.57050.3068264948291240.2083092047742691X-RAY DIFFRACTION99.4348286824
2.5705-2.640.3154748001341500.2104679825362709X-RAY DIFFRACTION99.3053143453
2.64-2.71770.2830512147531370.2103130366912679X-RAY DIFFRACTION99.4350282486
2.7177-2.80540.2766955569451540.2085805187492682X-RAY DIFFRACTION99.1955229101
2.8054-2.90560.2661525930491210.2091409981142724X-RAY DIFFRACTION99.6846531184
2.9056-3.0220.3274758899961250.2187618498262717X-RAY DIFFRACTION99.3011879804
3.022-3.15950.3174212918811430.2126451402542655X-RAY DIFFRACTION97.5933031043
3.1595-3.32610.2726371027541500.2132384705562722X-RAY DIFFRACTION99.9651931779
3.3261-3.53450.2595212740711510.1892460307772724X-RAY DIFFRACTION99.9652294854
3.5345-3.80740.2371779651191410.1669992829032765X-RAY DIFFRACTION99.8968717772
3.8074-4.19050.184031462281270.137964585982754X-RAY DIFFRACTION99.8959778086
4.1905-4.79670.1937402134951280.1267264898792795X-RAY DIFFRACTION99.795151929
4.7967-6.04280.1815970230371350.1501910727842749X-RAY DIFFRACTION97.7627118644
6.0428-70.18665272680.183872701321430.1354934225752924X-RAY DIFFRACTION99.3521218011

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