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- PDB-6k34: Crystal Structure of DphMB1 -

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Basic information

Entry
Database: PDB / ID: 6k34
TitleCrystal Structure of DphMB1
ComponentsLipase
KeywordsHYDROLASE / hycrolysis
Function / homology
Function and homology information


Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium sp. YC-RL4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFan, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31170119 China
CitationJournal: To Be Published
Title: Crystal Structure of DphMB1
Authors: Fan, S.
History
DepositionMay 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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
B: Lipase
A: Lipase
C: Lipase
D: Lipase


Theoretical massNumber of molelcules
Total (without water)135,5844
Polymers135,5844
Non-polymers00
Water3,837213
1
B: Lipase


Theoretical massNumber of molelcules
Total (without water)33,8961
Polymers33,8961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lipase


Theoretical massNumber of molelcules
Total (without water)33,8961
Polymers33,8961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipase


Theoretical massNumber of molelcules
Total (without water)33,8961
Polymers33,8961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipase


Theoretical massNumber of molelcules
Total (without water)33,8961
Polymers33,8961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.575, 159.539, 71.132
Angle α, β, γ (deg.)90.00, 105.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lipase


Mass: 33896.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium sp. YC-RL4 (bacteria) / Gene: A7U43_17735, dphMB1 / Plasmid: pColdII / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A172UPQ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Sodium chloride,Imidazole, Potassium/Sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97917 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 47483 / % possible obs: 98 % / Redundancy: 6.3 % / CC1/2: 0.969 / Net I/σ(I): 8.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.9 % / Num. unique obs: 4674 / CC1/2: 0.707 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QZ3

1qz3


Resolution: 2.5→39.837 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.72
RfactorNum. reflection% reflection
Rfree0.2526 2084 4.87 %
Rwork0.1866 --
obs0.1898 42826 89.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8968 0 0 213 9181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099204
X-RAY DIFFRACTIONf_angle_d1.18512656
X-RAY DIFFRACTIONf_dihedral_angle_d10.7595408
X-RAY DIFFRACTIONf_chiral_restr0.0681440
X-RAY DIFFRACTIONf_plane_restr0.0081680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.55820.3285930.2361740X-RAY DIFFRACTION58
2.5582-2.62220.32951120.23121927X-RAY DIFFRACTION64
2.6222-2.6930.28181050.23342126X-RAY DIFFRACTION70
2.693-2.77230.29741150.22312483X-RAY DIFFRACTION81
2.7723-2.86170.29871260.22562824X-RAY DIFFRACTION93
2.8617-2.9640.2961580.22412986X-RAY DIFFRACTION98
2.964-3.08260.30651640.21773002X-RAY DIFFRACTION99
3.0826-3.22280.29561410.2172981X-RAY DIFFRACTION98
3.2228-3.39270.30221620.21522973X-RAY DIFFRACTION98
3.3927-3.60510.2871490.20082815X-RAY DIFFRACTION93
3.6051-3.88320.24171570.16412899X-RAY DIFFRACTION96
3.8832-4.27360.21741540.16243009X-RAY DIFFRACTION99
4.2736-4.89110.22071420.15032989X-RAY DIFFRACTION98
4.8911-6.15860.21241550.16963026X-RAY DIFFRACTION99
6.1586-39.84170.18781510.16242962X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 25.5712 Å / Origin y: -7.8313 Å / Origin z: 16.6972 Å
111213212223313233
T0.2662 Å2-0.0098 Å20.0173 Å2-0.287 Å20.0341 Å2--0.2855 Å2
L-0.0136 °20.0218 °20.054 °2-0.1757 °2-0.0909 °2--0.1003 °2
S0.0352 Å °-0.0049 Å °-0.0059 Å °-0.0066 Å °-0.0375 Å °-0.0489 Å °0.0165 Å °0.0309 Å °0.0042 Å °
Refinement TLS groupSelection details: all

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