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- PDB-6a7w: Structure of a catalytic domain of the colistin resistance enzyme -

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Basic information

Entry
Database: PDB / ID: 6a7w
TitleStructure of a catalytic domain of the colistin resistance enzyme
ComponentsPutative integral membrane protein
KeywordsTRANSFERASE / colistin resistance / catalytic domain / HYDROLASE
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / plasma membrane
Similarity search - Function
Phosphoethanolamine transferase, N-terminal / Phosphoethanolamine transferase EptA/EptB / Phosphoethanolamine transferase / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative integral membrane protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.988 Å
AuthorsWang, X.D. / Chai, Y. / Qi, J.X. / Gao, G.F.
CitationJournal: Sci China Life Sci / Year: 2018
Title: Structural and functional insights into MCR-2 mediated colistin resistance.
Authors: Wang, X. / Lu, Q. / Qi, J. / Chai, Y. / Wang, Y. / Gao, G.F.
History
DepositionJul 4, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 7, 2018ID: 5XNU
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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
A: Putative integral membrane protein
B: Putative integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4174
Polymers72,2872
Non-polymers1312
Water0
1
A: Putative integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2092
Polymers36,1431
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2092
Polymers36,1431
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.443, 82.296, 79.914
Angle α, β, γ (deg.)90.00, 97.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative integral membrane protein


Mass: 36143.254 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcr-2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C3NEV1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.08 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M calcium acetate; 0.1 M MES, pH 6.0, 22% PEG 8000 (v/v), 0.03% DDM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.98→50 Å / Num. obs: 12018 / % possible obs: 99.2 % / Redundancy: 4 % / Rpim(I) all: 0.105 / Rsym value: 0.187 / Net I/σ(I): 7.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1228 / Rpim(I) all: 0.318 / Rsym value: 0.565 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K4P

5k4p


Resolution: 2.988→41.148 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 23.05
RfactorNum. reflection% reflection
Rfree0.2198 551 4.68 %
Rwork0.1798 --
obs0.1818 11775 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.988→41.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 0 0 5084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045216
X-RAY DIFFRACTIONf_angle_d0.7527082
X-RAY DIFFRACTIONf_dihedral_angle_d20.4671882
X-RAY DIFFRACTIONf_chiral_restr0.048776
X-RAY DIFFRACTIONf_plane_restr0.003932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.988-3.28860.31931420.23742571X-RAY DIFFRACTION89
3.2886-3.76410.23051350.19492862X-RAY DIFFRACTION99
3.7641-4.74130.19991420.15282881X-RAY DIFFRACTION99
4.7413-41.15190.19041320.17472910X-RAY DIFFRACTION98
Refinement TLS params.

S33: 0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4257-0.1125-0.00150.0810.2160.6512-00.0506-0.0292-0.02960.00460.0739-0.0127-0.00110.2682-0.01110.00210.26820.00790.275110.1936-17.449692.0505
20.4847-0.08310.06990.264-0.10360.56240.0099-0.0345-0.02980.0423-0.0077-0.0542-0.0410.0460.2767-0.00580.00470.27030.01370.2855-5.6149-55.2898104.3061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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