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- PDB-3gnl: Structure of uncharacterized protein (LMOf2365_1472) from Listeri... -

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Basic information

Entry
Database: PDB / ID: 3gnl
TitleStructure of uncharacterized protein (LMOf2365_1472) from Listeria monocytogenes serotype 4b
Componentsuncharacterized protein, DUF633, LMOf2365_1472
Keywordsstructural genomics / unknown function / uncharacterized protein / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyHelix Hairpins - #1890 / Vaccinia Virus protein VP39 / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta / :
Function and homology information
Biological speciesListeria monocytogenes str. 4b F2365 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of uncharacterized protein (LMOf2365_1472) from Listeria monocytogenes serotype 4b
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionMar 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein, DUF633, LMOf2365_1472
B: uncharacterized protein, DUF633, LMOf2365_1472


Theoretical massNumber of molelcules
Total (without water)55,2302
Polymers55,2302
Non-polymers00
Water8,269459
1
A: uncharacterized protein, DUF633, LMOf2365_1472


Theoretical massNumber of molelcules
Total (without water)27,6151
Polymers27,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein, DUF633, LMOf2365_1472


Theoretical massNumber of molelcules
Total (without water)27,6151
Polymers27,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.273, 84.802, 91.168
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsUnknown

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Components

#1: Protein uncharacterized protein, DUF633, LMOf2365_1472


Mass: 27614.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes str. 4b F2365 (bacteria)
Gene: LMOf2365_1472 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q71ZL7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Sodium Cacodylate pH 6.5, 30% PEG 6K , 0.2M Sodium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 81636 / % possible obs: 99.9 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.08 / Χ2: 1.413 / Net I/σ(I): 34.284
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.558.10.48780770.918100
1.55-1.628.60.39180400.947100
1.62-1.6990.29480810.987100
1.69-1.7810.20.22281111.06100
1.78-1.89130.16880881.206100
1.89-2.0413.10.11381461.415100
2.04-2.2413.10.08781461.653100
2.24-2.56130.08181721.791100
2.56-3.2312.90.07782771.854100
3.23-4011.90.0784981.69799.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
CCP4phasing
RefinementResolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.209 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.845 / SU B: 1.396 / SU ML: 0.053 / SU R Cruickshank DPI: 0.079 / SU Rfree: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.224 4088 5 %RANDOM
Rwork0.196 ---
obs0.198 81539 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.72 Å2 / Biso mean: 24.724 Å2 / Biso min: 10.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 0 459 4200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223817
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.955193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5385494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01425.723173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02715719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8061519
X-RAY DIFFRACTIONr_chiral_restr0.1170.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212851
X-RAY DIFFRACTIONr_mcbond_it1.48422370
X-RAY DIFFRACTIONr_mcangle_it2.38833856
X-RAY DIFFRACTIONr_scbond_it2.1721447
X-RAY DIFFRACTIONr_scangle_it3.43731326
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 274 -
Rwork0.271 5666 -
all-5940 -
obs--99.97 %

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