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- PDB-4tn0: Crystal Structure of the C-terminal Periplasmic Domain of Phospho... -

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Basic information

Entry
Database: PDB / ID: 4tn0
TitleCrystal Structure of the C-terminal Periplasmic Domain of Phosphoethanolamine Transferase EptC from Campylobacter jejuni
ComponentsUPF0141 protein yjdB
KeywordsTRANSFERASE / Alkaline phosphatase-like / Phosphoethanolamine transferase / Phosphothreonine / Periplasm
Function / homologyAlkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesCampylobacter jejuni subsp. jejuni HB93-13 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.4 Å
AuthorsFage, C.D. / Brown, D. / Boll, J.M. / Keatinge-Clay, A.T. / Trent, M.S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI064184 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI076322 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106112 United States
Army Research OfficeW911NF-12-1-0390 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystallographic study of the phosphoethanolamine transferase EptC required for polymyxin resistance and motility in Campylobacter jejuni.
Authors: Fage, C.D. / Brown, D.B. / Boll, J.M. / Keatinge-Clay, A.T. / Trent, M.S.
History
DepositionJun 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Jul 20, 2016Group: Data collection
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0141 protein yjdB
B: UPF0141 protein yjdB
C: UPF0141 protein yjdB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8316
Polymers110,6343
Non-polymers1963
Water32418
1
A: UPF0141 protein yjdB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9442
Polymers36,8781
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UPF0141 protein yjdB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9442
Polymers36,8781
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UPF0141 protein yjdB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9442
Polymers36,8781
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.850, 183.140, 121.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein UPF0141 protein yjdB


Mass: 36878.145 Da / Num. of mol.: 3 / Fragment: UNP residues 203-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni HB93-13 (Campylobacter)
Gene: CJJHB9313_0266 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3ZEY5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 200 mM diammonium phosphate, 15% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.268 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 4, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.268 Å / Relative weight: 1
ReflectionNumber: 392584 / Rmerge(I) obs: 0.112 / Χ2: 1.05 / D res high: 2.4 Å / Num. obs: 102491 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
7.5910.73209510.031
6.27.59273510.042
5.376.2321410.047
4.85.37365310.045
4.384.8403510.046
4.064.38437210.049
3.794.06469710.061
3.583.79500310.074
3.393.58530610.097
3.243.39555310.114
3.13.24585010.152
2.983.1605410.203
2.872.98633210.266
2.772.87656010.337
2.682.77673910.432
2.62.68699310.554
2.532.6716210.686
2.462.53742710.881
2.42.46756910.996
ReflectionResolution: 2.4→55 Å / Num. obs: 102491 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 39.51 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.13 / Χ2: 1.055 / Net I/σ(I): 10.63 / Num. measured all: 392584
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.4-2.460.6740.9961.4528951759975691.15699.6
2.46-2.530.6960.8811.5728374745774271.02399.6
2.53-2.60.7720.686227374718271620.79799.7
2.6-2.680.8210.5542.5926079703469930.64799.4
2.68-2.770.8980.4323.0325916676367390.50299.6
2.77-2.870.9290.3373.925408656665600.39199.9
2.87-2.980.950.2664.9524559633863320.30999.9
2.98-3.10.970.2036.5423466605960540.23599.9
3.1-3.240.9810.1528.6922656585458500.17799.9
3.24-3.390.9890.11411.5621455556055530.13299.9
3.39-3.580.9910.09713.8319922533153060.11399.5
3.58-3.790.9940.07417.3418690502350030.08699.6
3.79-4.060.9960.06119.9517372472946970.07199.3
4.06-4.380.9970.04923.2816891437643720.05799.9
4.38-4.80.9970.04625.0915538403740350.053100
4.8-5.370.9980.04525.1814178365636530.05399.9
5.37-6.20.9970.04723.4112528321532140.055100
6.2-7.590.9980.04225.6510658273527350.049100
7.59-10.730.9980.03132.148164209520950.035100
10.730.9980.02635.474405116411420.03198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.29 Å54.58 Å
Translation2.29 Å54.58 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHENIXphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→54.58 Å / FOM work R set: 0.7749 / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 2703 5.07 %Random selection
Rwork0.2147 97250 --
obs0.2168 102446 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.19 Å2 / Biso mean: 49.77 Å2 / Biso min: 19.33 Å2
Refinement stepCycle: final / Resolution: 2.4→54.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7390 0 3 18 7411
Biso mean--35.23 38.75 -
Num. residues----923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097570
X-RAY DIFFRACTIONf_angle_d1.28410234
X-RAY DIFFRACTIONf_chiral_restr0.0561115
X-RAY DIFFRACTIONf_plane_restr0.0061303
X-RAY DIFFRACTIONf_dihedral_angle_d14.2852766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.42720.38021730.32983266343999
2.4272-2.45580.38451680.320432073375100
2.4558-2.48580.35451880.32613229341799
2.4858-2.51720.35321600.301832583418100
2.5172-2.55030.32861620.298232353397100
2.5503-2.58530.32161710.294232663437100
2.5853-2.62220.3391870.306632443431100
2.6222-2.66130.35851910.32013162335399
2.6613-2.70290.39131550.32233251340699
2.7029-2.74720.35641820.289532583440100
2.7472-2.79460.29911500.265232373387100
2.7946-2.84540.33621500.26832513401100
2.8454-2.90020.31771740.266433193493100
2.9002-2.95930.30471970.267332113408100
2.9593-3.02370.29791990.275831923391100
3.0237-3.0940.33291900.274932593449100
3.094-3.17140.32461710.273532103381100
3.1714-3.25710.32691740.248932643438100
3.2571-3.3530.26031850.236332433428100
3.353-3.46120.3121600.23853230339099
3.4612-3.58480.28851780.232532623440100
3.5848-3.72830.2241450.20683238338399
3.7283-3.8980.23291430.18753275341899
3.898-4.10340.21161840.18132283412100
4.1034-4.36040.19291820.156132283410100
4.3604-4.69690.16351500.143632823432100
4.6969-5.16930.19491990.14831983397100
5.1693-5.91650.2171920.163632393431100
5.9165-7.45120.21231430.163533033446100
7.4512-54.59410.16541930.14433205339899

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