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- PDB-5k4p: Catalytic Domain of MCR-1 phosphoethanolamine transferase -

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Basic information

Entry
Database: PDB / ID: 5k4p
TitleCatalytic Domain of MCR-1 phosphoethanolamine transferase
ComponentsProbable phosphatidylethanolamine transferase Mcr-1
KeywordsTRANSFERASE / phosphoethanolamine transferase / alpha/beta/alpha fold / alkaline phosphatase superfamily
Function / homology
Function and homology information


phosphotransferase activity, phosphate group as acceptor / Transferases; Transferring phosphorus-containing groups / lipopolysaccharide core region biosynthetic process / response to antibiotic / 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
sorbitol / Probable phosphatidylethanolamine transferase Mcr-1
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.318 Å
AuthorsStojanoski, V. / Palzkill, T. / Prasad, B.V.V. / Sankaran, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Bmc Biol. / Year: 2016
Title: Structure of the catalytic domain of the colistin resistance enzyme MCR-1.
Authors: Stojanoski, V. / Sankaran, B. / Prasad, B.V. / Poirel, L. / Nordmann, P. / Palzkill, T.
History
DepositionMay 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,34512
Polymers38,5091
Non-polymers83611
Water6,612367
1
A: Probable phosphatidylethanolamine transferase Mcr-1
hetero molecules

A: Probable phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,69024
Polymers77,0182
Non-polymers1,67322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3080 Å2
ΔGint-473 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.080, 59.080, 186.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1010-

HOH

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Components

#1: Protein Probable phosphatidylethanolamine transferase Mcr-1 / Polymyxin resistance protein MCR-1


Mass: 38508.914 Da / Num. of mol.: 1 / Fragment: Catalytic Domain (UNP residues 214-541) / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Plasmid details: pET28a / Strain: BL21(DE3)
References: UniProt: A0A0R6L508, Transferases; Transferring phosphorus-containing groups
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Sugar ChemComp-SOR / sorbitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M zinc acetate dihydrate, 0.1 M sodium cacodylate trihydrate pH 6.5, 3% w/v D-Sorbitol, and 18% PEG 8,000
PH range: 6.5 -7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2016
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.318→56.327 Å / Num. all: 79227 / Num. obs: 79227 / % possible obs: 100 % / Redundancy: 14.7 % / Biso Wilson estimate: 9.84 Å2 / Rpim(I) all: 0.055 / Rrim(I) all: 0.212 / Rsym value: 0.197 / Net I/av σ(I): 2.859 / Net I/σ(I): 10.1 / Num. measured all: 1161283
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.32-1.3911.71.7630.4132914113700.5521.91.7631.8100
1.39-1.4714.51.1520.6156522107660.3191.2221.1523100
1.47-1.5815.60.7021157926101440.1870.7430.7024.8100
1.58-1.715.60.4691.514768594780.1250.4980.4696.6100
1.7-1.8615.60.2842.513624987570.0760.3030.2849.6100
1.86-2.0815.50.1684.112294579530.0460.1820.16814.3100
2.08-2.4115.30.129510807970800.0360.1410.12918.1100
2.41-2.9514.50.12258794360620.0340.1320.12220.1100
2.95-4.1714.70.1015.67012447860.0280.1090.10124.7100
4.17-56.32714.40.0964089628310.0250.0970.0924.999.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALA3.3.22data scaling
SHELXphasing
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.318→49.92 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.64 / Phase error: 16.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1776 7369 4.94 %RANDOM
Rwork0.1544 141655 --
obs0.1555 79227 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.01 Å2 / Biso mean: 15.354 Å2 / Biso min: 5.52 Å2
Refinement stepCycle: final / Resolution: 1.318→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 22 368 2931
Biso mean--11.04 26.86 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142614
X-RAY DIFFRACTIONf_angle_d1.3623552
X-RAY DIFFRACTIONf_chiral_restr0.107394
X-RAY DIFFRACTIONf_plane_restr0.009463
X-RAY DIFFRACTIONf_dihedral_angle_d14.146950
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.318-1.3330.34742490.305347184967
1.333-1.34870.29062750.286546974972
1.3487-1.36510.30882350.280847354970
1.3651-1.38240.28832340.262347544988
1.3824-1.40060.27072530.249147154968
1.4006-1.41980.24622630.23247074970
1.4198-1.44010.23292320.217147624994
1.4401-1.46160.23042110.200147074918
1.4616-1.48440.18762710.193447124983
1.4844-1.50870.19782440.180346654909
1.5087-1.53480.21252750.177747305005
1.5348-1.56270.19972410.169347064947
1.5627-1.59270.17742660.15647244990
1.5927-1.62520.18442490.15147054954
1.6252-1.66060.15352140.146247524966
1.6606-1.69920.17992740.138246904964
1.6992-1.74170.16092760.133747134989
1.7417-1.78880.17332190.135547444963
1.7888-1.84140.17852260.137847354961
1.8414-1.90090.13482390.1347404979
1.9009-1.96880.15932410.130647524993
1.9688-2.04760.15612840.131246704954
2.0476-2.14080.16362460.134446974943
2.1408-2.25370.16862540.133647144968
2.2537-2.39490.18562520.140547264978
2.3949-2.57980.16342300.144247304960
2.5798-2.83940.15512730.143347094982
2.8394-3.25020.15272200.143947134933
3.2502-4.09460.15412160.132747654981
4.0946-49.95630.15842070.144747684975
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9651-0.3936-0.330.59950.17140.489-0.00180.01270.0094-0.03350.0126-0.03740.02710.00680.00410.0683-0.0101-0.00010.0595-0.00010.063125.1741-1.899452.4205
20.798-0.4554-0.64180.68970.40260.7012-0.0477-0.16420.05640.12130.0989-0.11380.03380.1506-0.04480.08850.0081-0.01380.1019-0.01520.095430.34312.119965.6033
36.15193.5173-1.49917.6285-1.35583.33380.0039-0.4203-0.2120.5052-0.07930.42330.1998-0.23170.07950.16040.00260.060.1949-0.01950.16464.416.35872.433
40.5564-0.1854-0.08840.84750.22650.4951-0.0022-0.0060.0789-0.04470.0249-0.0111-0.0282-0.0084-0.02330.0551-0.00150.00450.05090.00340.060418.56654.922357.7209
53.2896-0.3196-0.03541.182-0.04930.26890.08020.27670.0221-0.1635-0.0669-0.0656-0.0439-0.003-0.01320.10080.00730.01890.1017-0.00110.066927.5061-1.392342.8794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 218 through 311 )A218 - 311
2X-RAY DIFFRACTION2chain 'A' and (resid 312 through 407 )A312 - 407
3X-RAY DIFFRACTION3chain 'A' and (resid 408 through 423 )A408 - 423
4X-RAY DIFFRACTION4chain 'A' and (resid 424 through 502 )A424 - 502
5X-RAY DIFFRACTION5chain 'A' and (resid 503 through 541 )A503 - 541

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