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- PDB-5u8j: Crystal structure of a protein of unknown function ECL_02571 invo... -

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Basic information

Entry
Database: PDB / ID: 5u8j
TitleCrystal structure of a protein of unknown function ECL_02571 involved in membrane biogenesis from Enterobacter cloacae
ComponentsUPF0502 protein BFJ73_07745
KeywordsUNKNOWN FUNCTION / membrane biogenesis / alpha/beta protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsStogios, P.J. / Skarina, T. / Sandoval, J. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: Crystal structure of a protein of unknown function ECL_02571 involved in membrane biogenesis from Enterobacter cloacae
Authors: Stogios, P.J.
History
DepositionDec 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: UPF0502 protein BFJ73_07745
B: UPF0502 protein BFJ73_07745
C: UPF0502 protein BFJ73_07745
D: UPF0502 protein BFJ73_07745
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4256
Polymers79,3544
Non-polymers712
Water3,999222
1
A: UPF0502 protein BFJ73_07745
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8742
Polymers19,8381
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UPF0502 protein BFJ73_07745


Theoretical massNumber of molelcules
Total (without water)19,8381
Polymers19,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UPF0502 protein BFJ73_07745
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8742
Polymers19,8381
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: UPF0502 protein BFJ73_07745


Theoretical massNumber of molelcules
Total (without water)19,8381
Polymers19,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.170, 53.890, 90.000
Angle α, β, γ (deg.)90.00, 100.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
UPF0502 protein BFJ73_07745


Mass: 19838.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: BFJ73_07745 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: A0A1B3EZY2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20% PEG3350, 0.2 M potassium dihydrogen phosphate, 1% sucrose, 0.1 M phosphate citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.52→30 Å / Num. obs: 28186 / % possible obs: 98.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 19.84
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 2.17 / CC1/2: 0.664 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BZ6

3bz6


Resolution: 2.52→29.564 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2737 1361 4.92 %RANDOM
Rwork0.2126 ---
obs0.2157 27685 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→29.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5326 0 2 222 5550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035419
X-RAY DIFFRACTIONf_angle_d0.6547313
X-RAY DIFFRACTIONf_dihedral_angle_d23.6342087
X-RAY DIFFRACTIONf_chiral_restr0.042831
X-RAY DIFFRACTIONf_plane_restr0.003962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5201-2.61010.34351180.28252582X-RAY DIFFRACTION97
2.6101-2.71450.36721490.28032555X-RAY DIFFRACTION97
2.7145-2.8380.3661560.29072549X-RAY DIFFRACTION97
2.838-2.98750.35041010.26632647X-RAY DIFFRACTION98
2.9875-3.17440.32031270.24872613X-RAY DIFFRACTION98
3.1744-3.41920.27791270.22162630X-RAY DIFFRACTION99
3.4192-3.76270.27491390.21392641X-RAY DIFFRACTION99
3.7627-4.30570.25571460.17522661X-RAY DIFFRACTION99
4.3057-5.41930.20521440.1762695X-RAY DIFFRACTION99
5.4193-29.56560.25911540.1972751X-RAY DIFFRACTION100
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)
11.80791.79321.46753.69272.86612.23110.6870.6549-0.5374-0.39350.1002-0.23980.28360.75491.28481.3072-0.30830.35580.3516-0.62030.11991.05544.335417.3629
22.90391.56670.57345.12470.86091.656-0.38560.08880.3001-0.38440.39380.7266-0.2985-0.28650.00030.4484-0.0729-0.01640.40030.04350.4144-10.90388.502328.1457
31.0288-1.399-0.80411.91691.07510.61680.11481.17111.0921-2.6050.60470.9966-0.96210.11180.1861.0171-0.1912-0.06770.6940.19460.481-10.8834-3.653115.7631
43.0911-0.0023-0.46474.76620.58971.4273-0.33440.0126-0.50610.36950.6917-0.90840.29650.43040.00140.4861-0.0115-0.04960.4963-0.17090.55071.6968-9.489130.2105
52.00264.0258-1.42562.2869-0.91050.3781-0.26180.9063-2.1854-0.4485-0.8987-0.8571.1483-0.2244-0.21771.2448-0.03520.3590.3333-0.07860.75926.31211.065516.256
64.37710.2411-1.18031.33090.41642.7828-0.1844-0.0815-0.05960.13690.2256-0.06160.1136-0.0168-00.4377-0.07450.02160.3724-0.05790.35877.812624.028323.6398
73.9292-0.0824-2.66872.32512.01723.59520.10550.38750.1634-0.2902-0.0492-0.31030.0881-0.35850.00060.4279-0.13340.03310.4734-0.02110.42313.465724.607610.0825
80.70280.3266-0.97031.436-0.05561.33060.49320.19670.2453-0.58530.1346-0.00870.4144-0.57120.00040.6954-0.1652-0.0290.7542-0.0150.41783.963616.98671.5928
91.55071.14720.44073.2288-1.39822.6503-0.28990.2403-0.1253-0.30950.39390.25420.2341-0.268800.4234-0.13290.00860.49320.04120.4505-28.2618-16.782821.0171
101.2301-0.39910.62020.7182-0.08250.40090.19420.2966-0.0711-0.5194-0.03590.4006-0.6679-0.1069-0.00190.5612-0.1144-0.06960.60550.11930.5622-28.172-6.062915.1574
114.95230.46070.1312.45852.13864.35210.0262-0.4473-0.25490.4276-0.0570.0120.3523-0.49590.00140.4831-0.0760.00950.50010.1120.4133-27.674-12.967639.8348
124.4286-2.1187-4.31934.37122.58434.29560.1434-1.5597-0.66911.7132-0.23581.65910.7954-1.7801-0.15570.5818-0.13840.05231.39050.28360.8138-41.2935-14.910735.4346
13-00.00420.0070.00110.01670.04560.4577-0.47990.19830.66290.39070.5858-0.6019-0.1587-01.00570.01690.3671.0134-0.09360.951538.627841.621327.1438
143.5732-0.11590.58582.76380.77050.9143-0.02390.3-0.0460.1057-0.0461-0.0227-0.06050.320200.4261-0.178-0.04880.5760.05340.574636.787229.827415.5965
153.0138-0.2233-0.75873.30371.75331.1530.07610.05861.6741-0.2125-0.32610.1963-0.1102-0.1938-0.00010.4682-0.0224-0.16570.58310.13671.090823.807643.101414.3065
161.1318-0.8203-0.09191.243-0.43450.398-0.58270.22951.75180.26670.17350.3984-0.5591-0.029-0.03910.6341-0.2738-0.23770.24160.13351.90331.124550.154219.7806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:5)
2X-RAY DIFFRACTION2(chain A and resid 6:84)
3X-RAY DIFFRACTION3(chain A and resid 85:94)
4X-RAY DIFFRACTION4(chain A and resid 95:171)
5X-RAY DIFFRACTION5(chain B and resid 1:7)
6X-RAY DIFFRACTION6(chain B and resid 8:71)
7X-RAY DIFFRACTION7(chain B and resid 72:141)
8X-RAY DIFFRACTION8(chain B and resid 142:173)
9X-RAY DIFFRACTION9(chain C and resid 2:63)
10X-RAY DIFFRACTION10(chain C and resid 64:86)
11X-RAY DIFFRACTION11(chain C and resid 87:166)
12X-RAY DIFFRACTION12(chain C and resid 167:172)
13X-RAY DIFFRACTION13(chain D and resid 1:5)
14X-RAY DIFFRACTION14(chain D and resid 6:86)
15X-RAY DIFFRACTION15(chain D and resid 87:142)
16X-RAY DIFFRACTION16(chain D and resid 143:171)

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