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- PDB-6kxh: Alp1U_Y247F mutant in complex with Fluostatin C -

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Basic information

Entry
Database: PDB / ID: 6kxh
TitleAlp1U_Y247F mutant in complex with Fluostatin C
ComponentsPutative hydrolase
KeywordsHYDROLASE / Hydrolyse epoxide / Cis-vicinal diol
Function / homology
Function and homology information


epoxide hydrolase activity
Similarity search - Function
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
Fluostatin C / D-MALATE / Putative hydrolase / Putative hydrolase
Similarity search - Component
Biological speciesStreptomyces ambofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78039550258 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 11, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ncs_dom_lim.selection_details

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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)149,77413
Polymers148,1404
Non-polymers1,6349
Water13,872770
1
A: Putative hydrolase
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0107
Polymers74,0702
Non-polymers9405
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-33 kcal/mol
Surface area20850 Å2
MethodPISA
2
B: Putative hydrolase
C: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7646
Polymers74,0702
Non-polymers6954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-45 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.477, 101.562, 117.481
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 27 - 318 / Label seq-ID: 47 - 338

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A' and segid 'AA 'AA
22chain 'B' and segid 'BA 'BB
33chain 'C' and segid 'CA 'CC
44chain 'D' and segid 'DA 'DD

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Components

#1: Protein
Putative hydrolase / / epoxy hydrolase Alp1U


Mass: 37034.914 Da / Num. of mol.: 4 / Mutation: Y247F
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-DY9 / Fluostatin C


Mass: 324.284 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C18H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.96 Å3/Da / Density % sol: 37.33 %
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: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.78→31.98 Å / Num. obs: 111803 / % possible obs: 99.88 % / Redundancy: 1.1 % / Biso Wilson estimate: 26.4165605827 Å2 / CC1/2: 1 / Net I/σ(I): 16.18
Reflection shellResolution: 1.78→1.844 Å / Num. unique obs: 10937 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78039550258→31.98 Å / SU ML: 0.176324970921 / Cross valid method: FREE R-VALUE / σ(F): 1.33648905052 / Phase error: 21.5299516835
RfactorNum. reflection% reflection
Rfree0.206190980071 5551 4.96791573069 %
Rwork0.169879528531 --
obs0.171638507138 111737 99.8275708032 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.0944132075 Å2
Refinement stepCycle: LAST / Resolution: 1.78039550258→31.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9109 0 117 770 9996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006880169601089515
X-RAY DIFFRACTIONf_angle_d1.0870914076712984
X-RAY DIFFRACTIONf_chiral_restr0.04703516987491353
X-RAY DIFFRACTIONf_plane_restr0.005253213439891796
X-RAY DIFFRACTIONf_dihedral_angle_d12.64759066253448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7804-1.80060.2846336762511670.226202555133404X-RAY DIFFRACTION97.728516694
1.8006-1.82180.2757149653251900.2127827740113477X-RAY DIFFRACTION100
1.8218-1.8440.2542767877011890.2110281649123508X-RAY DIFFRACTION99.9729583559
1.844-1.86740.2559367936551900.201448039753498X-RAY DIFFRACTION99.9728923828
1.8674-1.89190.2328870729291860.1981530492933549X-RAY DIFFRACTION100
1.8919-1.91780.3126007840372000.277113016443471X-RAY DIFFRACTION99.9727668845
1.9178-1.94520.2804872933451680.2418460317133527X-RAY DIFFRACTION99.9729437229
1.9452-1.97430.2373202563871840.1991557289873500X-RAY DIFFRACTION100
1.9743-2.00510.2268800245381920.1838777167233508X-RAY DIFFRACTION100
2.0051-2.0380.2071285832351780.1855884467443539X-RAY DIFFRACTION100
2.038-2.07310.2105805607391680.1912321966323535X-RAY DIFFRACTION100
2.0731-2.11080.2242072917891720.1865372617883516X-RAY DIFFRACTION100
2.1108-2.15140.2281722829661840.1822570719473525X-RAY DIFFRACTION100
2.1514-2.19530.2395865084511970.1882820824533491X-RAY DIFFRACTION100
2.1953-2.2430.2503363488851970.2077687920243520X-RAY DIFFRACTION99.8656636217
2.243-2.29520.2735417874051920.227041311433504X-RAY DIFFRACTION99.8109640832
2.2952-2.35260.220885323371710.182060016183581X-RAY DIFFRACTION100
2.3526-2.41620.223381490731860.1820278100373521X-RAY DIFFRACTION100
2.4162-2.48720.2541212949881800.1894914103173516X-RAY DIFFRACTION100
2.4872-2.56750.2030275547831920.1757736690263543X-RAY DIFFRACTION100
2.5675-2.65920.2120614891951840.1802639918423554X-RAY DIFFRACTION100
2.6592-2.76560.2157379045071950.1760245921313528X-RAY DIFFRACTION100
2.7656-2.89140.2186872491242180.176031740123531X-RAY DIFFRACTION99.9733333333
2.8914-3.04370.2209142547831920.1831245058533569X-RAY DIFFRACTION100
3.0437-3.23430.2254804927921950.1872498137053542X-RAY DIFFRACTION99.9732477261
3.2343-3.48370.2393401347451660.1741193577423605X-RAY DIFFRACTION99.9469917837
3.4837-3.83380.1517682161671780.147833759343595X-RAY DIFFRACTION100
3.8338-4.38730.1351215793141890.1295704773123617X-RAY DIFFRACTION99.9474789916
4.3873-5.52290.1674419566051750.1291689971933668X-RAY DIFFRACTION99.8441153546
5.5229-31.980.1825880207881760.1439679097653744X-RAY DIFFRACTION97.9510244878
Refinement TLS params.Method: refined / Origin x: -1.71138396348 Å / Origin y: -26.4759493579 Å / Origin z: 43.6857442894 Å
111213212223313233
T0.187147372425 Å20.00207664137838 Å20.0448859643273 Å2-0.137055835854 Å2-0.0155288263097 Å2--0.233434411021 Å2
L0.568541040022 °2-0.0614528378602 °20.51008271095 °2-0.281029109074 °2-0.192937995422 °2--0.880273839653 °2
S-0.00871541929972 Å °0.0371608391372 Å °0.0691046328591 Å °0.0265522948218 Å °-0.0224148582958 Å °-0.0328327211432 Å °-0.0961083645245 Å °0.0963162320039 Å °0.0245130963067 Å °
Refinement TLS groupSelection details: all

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