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- PDB-7clz: Crystal structure of Alp1U W187F/Y247F in complex with fluostatin C -

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Basic information

Entry
Database: PDB / ID: 7clz
TitleCrystal structure of Alp1U W187F/Y247F in complex with fluostatin C
ComponentsPutative hydrolase
KeywordsHYDROLASE / Substrate / Complex / Biosynthesis
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
BORIC ACID / Fluostatin C / D-MALATE / Putative hydrolase / Putative hydrolase
Similarity search - Component
Biological speciesStreptomyces ambofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10001009432 Å
AuthorsZhang, L. / De, B.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)41606193 China
National Natural Science Foundation of China (NSFC)31820103003 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
DepositionJul 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 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 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)149,66215
Polymers147,9844
Non-polymers1,67911
Water6,377354
1
A: Putative hydrolase
C: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8597
Polymers73,9922
Non-polymers8675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-33 kcal/mol
Surface area20730 Å2
MethodPISA
2
B: Putative hydrolase
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8038
Polymers73,9922
Non-polymers8116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-29 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.664, 100.208, 117.45
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

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative hydrolase / Alp1U


Mass: 36995.879 Da / Num. of mol.: 4 / Mutation: W187F/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 (E. coli) / References: UniProt: Q1RQU8, UniProt: A0A0K2AJY3*PLUS

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Non-polymers , 5 types, 365 molecules

#2: Chemical ChemComp-DY9 / Fluostatin C


Mass: 324.284 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5
#5: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH3O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.92 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 277 K / Method: evaporation, recrystallization / pH: 5 / Details: 0.1M MMT pH 5.0, 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: 2.1→44.7 Å / Num. obs: 67180 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 31.1725963355 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.03037 / Net I/σ(I): 8.58
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.188 / Num. unique obs: 13302 / CC1/2: 0.943

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
XDS1.9_1692+SVNdata reduction
Aimless1.9_1692+SVNdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R3V

3r3v


Resolution: 2.10001009432→44.6955286937 Å / SU ML: 0.257410355092 / Cross valid method: FREE R-VALUE / σ(F): 1.33333610876 / Phase error: 26.0179731682
RfactorNum. reflection% reflection
Rfree0.246759656734 3482 5.20314998282 %
Rwork0.193154415534 63439 -
obs0.195874909575 66921 99.596678176 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.518325445 Å2
Refinement stepCycle: LAST / Resolution: 2.10001009432→44.6955286937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9078 0 118 354 9550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008505127438179455
X-RAY DIFFRACTIONf_angle_d1.1721480163812882
X-RAY DIFFRACTIONf_chiral_restr0.04964837956071348
X-RAY DIFFRACTIONf_plane_restr0.006295641381581765
X-RAY DIFFRACTIONf_dihedral_angle_d13.02995817243404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.10001009432-2.12880.2891984021931490.2167162025342483X-RAY DIFFRACTION100
2.1288-2.15920.3016708654611540.2191381678632497X-RAY DIFFRACTION99.8869630746
2.1592-2.19140.3213008795881410.2136703933272527X-RAY DIFFRACTION99.8129442574
2.1914-2.22570.2662815755711370.2188900644882512X-RAY DIFFRACTION99.8868778281
2.2257-2.26210.2925148396671320.21775112992502X-RAY DIFFRACTION99.8483699773
2.2621-2.30120.28413976522990.2106205512532560X-RAY DIFFRACTION99.5880149813
2.3012-2.3430.3380402214021380.2120739844822509X-RAY DIFFRACTION99.7362471741
2.343-2.38810.2780328085731360.2194011850462507X-RAY DIFFRACTION99.8111782477
2.3881-2.43680.2934912377541490.2227777732822497X-RAY DIFFRACTION99.4363021421
2.4368-2.48980.3062678202931510.2285422656262515X-RAY DIFFRACTION99.5519044063
2.4898-2.54770.2769845314661610.2163502524322486X-RAY DIFFRACTION99.5861550038
2.5477-2.61140.2985844087311390.2093695627792535X-RAY DIFFRACTION99.6274217586
2.6114-2.6820.2565327111231300.2111304863952517X-RAY DIFFRACTION99.1757212439
2.682-2.76090.3351313615541320.2318932195642466X-RAY DIFFRACTION97.157816006
2.7609-2.850.2343694921481400.2077835776882522X-RAY DIFFRACTION99.5512341062
2.85-2.95180.2644873869581430.2084932272312518X-RAY DIFFRACTION99.7376311844
2.9518-3.070.2743142199841450.2045518649612523X-RAY DIFFRACTION99.552238806
3.07-3.20970.2717141459521240.2043154926522548X-RAY DIFFRACTION99.4417566059
3.2097-3.37890.2460536983571250.2077307140662565X-RAY DIFFRACTION99.7774480712
3.3789-3.59050.250212667161360.1902842952132577X-RAY DIFFRACTION99.7793306363
3.5905-3.86750.2195376718451700.1809010311222542X-RAY DIFFRACTION99.9263080324
3.8675-4.25650.1830606392631170.1676136628052588X-RAY DIFFRACTION100
4.2565-4.87180.1824971795471440.1600085777632581X-RAY DIFFRACTION99.8168498168
4.8718-6.13540.2281009978771550.1847456611172615X-RAY DIFFRACTION99.8918139199
6.1354-8.040.2407309576241350.1653480614492747X-RAY DIFFRACTION99.4478951001
Refinement TLS params.Method: refined / Origin x: -1.2626868985 Å / Origin y: -26.2364096548 Å / Origin z: 43.8728428254 Å
111213212223313233
T0.157304778507 Å2-0.00504611057269 Å20.0262523653632 Å2-0.190102432602 Å2-0.0271040840616 Å2--0.200184644162 Å2
L0.6453258877 °2-0.266877385449 °20.205953344079 °2-0.578166975066 °2-0.26943195837 °2--0.602380347254 °2
S0.00349621416262 Å °0.0542439973614 Å °0.0386054953772 Å °0.00899559571234 Å °0.003803610478 Å °-0.0573304013317 Å °-0.0486486248197 Å °0.0812411201753 Å °-0.0137723652062 Å °
Refinement TLS groupSelection details: all

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