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- PDB-4zy7: Crystal structure of a Mycobacterial protein -

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Basic information

Entry
Database: PDB / ID: 4zy7
TitleCrystal structure of a Mycobacterial protein
ComponentsUncharacterized protein MSMEG_5817
KeywordsUNKNOWN FUNCTION / monomer / psi-loop / mycobacterium smegmatis
Function / homologyNonspecific Lipid-transfer Protein; Chain A - #40 / Bacterial SCP orthologue / Bacterial SCP ortholog / Nonspecific Lipid-transfer Protein; Chain A / 2-Layer Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / Bacterial SCP orthologue domain-containing protein
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShahine, A. / Rossjohn, J. / Beddoe, T.
CitationJournal: To Be Published
Title: Crystal structure of a Mycobacterial protein
Authors: Shahine, A. / Rossjohn, J. / Beddoe, T.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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: Uncharacterized protein MSMEG_5817
B: Uncharacterized protein MSMEG_5817
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1839
Polymers30,5732
Non-polymers6117
Water4,972276
1
A: Uncharacterized protein MSMEG_5817
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7296
Polymers15,2861
Non-polymers4425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein MSMEG_5817
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4553
Polymers15,2861
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.610, 70.490, 100.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-416-

HOH

DetailsMonomer according to size exclusion chromatography

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Components

#1: Protein Uncharacterized protein MSMEG_5817


Mass: 15286.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5817, MSMEI_5660, LJ00_28765 / Plasmid: pJAM2
Production host: Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain (production host): MC2 155 / References: UniProt: A0R4F7
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.04 % / Description: plate-like crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 16% PEG 6000, 0.1M Tris-HCl pH 8.3, 0.2M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.7→30.22 Å / Num. obs: 33734 / % possible obs: 99.2 % / Redundancy: 7 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 4.8 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALAdata scaling
iMOSFLMdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NSS

4nss


Resolution: 1.7→30.22 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 1707 5.07 %
Rwork0.175 --
obs0.177 33692 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→30.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 40 276 2128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051954
X-RAY DIFFRACTIONf_angle_d1.0652678
X-RAY DIFFRACTIONf_dihedral_angle_d12.7726
X-RAY DIFFRACTIONf_chiral_restr0.04323
X-RAY DIFFRACTIONf_plane_restr0.005349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.29191260.21582505X-RAY DIFFRACTION94
1.75-1.80650.23631450.19592610X-RAY DIFFRACTION99
1.8065-1.87110.20481400.1832653X-RAY DIFFRACTION100
1.8711-1.9460.20891410.17092650X-RAY DIFFRACTION100
1.946-2.03450.22081340.17452649X-RAY DIFFRACTION100
2.0345-2.14170.21551540.17472652X-RAY DIFFRACTION100
2.1417-2.27590.19931520.16852664X-RAY DIFFRACTION100
2.2759-2.45150.21441290.1642691X-RAY DIFFRACTION100
2.4515-2.69810.21981630.18182671X-RAY DIFFRACTION100
2.6981-3.08820.2341210.18032741X-RAY DIFFRACTION100
3.0882-3.88950.19011640.17012731X-RAY DIFFRACTION100
3.8895-30.22970.19741380.17292768X-RAY DIFFRACTION96
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)
11.8973-0.2336-0.2142.55650.713.57880.088-0.0342-0.04270.1019-0.12950.25270.0751-0.10750.00770.1242-0.02160.03010.1225-0.05780.1605-6.871618.1658-13.1049
22.6462-1.8476-2.32561.34561.30973.83590.18720.2475-0.1855-0.395-0.20860.1023-0.5042-0.2829-0.12330.20220.0431-0.01120.1675-0.0510.1637-5.631823.023-21.0087
31.43780.1126-0.1482.7519-0.89413.1692-0.1303-0.1666-0.06730.0155-0.0349-0.31090.10920.32830.07410.10420.02220.01080.16240.02710.12584.84725.588710.1378
42.5707-1.24761.55743.1245-0.86342.1649-0.0179-0.122-0.4081-0.10380.10540.23240.2646-0.267-0.09850.1175-0.01430.01080.1170.02630.1316-5.559820.86936.913
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 8 THROUGH 103 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 104 THROUGH 126 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID -6 THROUGH 102 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 103 THROUGH 126 )

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