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- PDB-4k15: 2.75 Angstrom Crystal Structure of Hypothetical Protein lmo2686 f... -

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Basic information

Entry
Database: PDB / ID: 4k15
Title2.75 Angstrom Crystal Structure of Hypothetical Protein lmo2686 from Listeria monocytogenes EGD-e
ComponentsLmo2686 protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyImmunoglobulin-like - #3860 / Lmo2686-like / Domain of unknown function DUF5626 / Domain of unknown function (DUF5626) / Immunoglobulin-like / Sandwich / Mainly Beta / Lmo2686 protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsMinasov, G. / Wawrzak, Z. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.75 Angstrom Crystal Structure of Hypothetical Protein lmo2686 from Listeria monocytogenes EGD-e
Authors: Minasov, G. / Wawrzak, Z. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo2686 protein
B: Lmo2686 protein
C: Lmo2686 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7825
Polymers58,7113
Non-polymers712
Water1,76598
1
A: Lmo2686 protein
B: Lmo2686 protein
C: Lmo2686 protein
hetero molecules

A: Lmo2686 protein
B: Lmo2686 protein
C: Lmo2686 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,56510
Polymers117,4236
Non-polymers1424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area17400 Å2
ΔGint-99 kcal/mol
Surface area40270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.093, 91.093, 125.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Lmo2686 protein


Mass: 19570.484 Da / Num. of mol.: 3 / Fragment: UNP residues 27-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: lmo2686 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q8Y3Z3
#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.: 98 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 7.2 mg/mL protein in 0.5 M sodium chloride, 0.1 M Tris-HCl, pH 8.3 against Classics II screen (A9): 0.1 M Bis-Tris, pH 5.5, 3 M sodium chloride, cryoprotectant: paratone, VAPOR DIFFUSION, ...Details: 7.2 mg/mL protein in 0.5 M sodium chloride, 0.1 M Tris-HCl, pH 8.3 against Classics II screen (A9): 0.1 M Bis-Tris, pH 5.5, 3 M sodium chloride, cryoprotectant: paratone, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97911 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 28, 2013 / Details: mirrors
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. all: 16172 / Num. obs: 16172 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 79.3 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 23.6
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.7 / Num. unique all: 787 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→29.82 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 23.345 / SU ML: 0.21
Isotropic thermal model: THERMAL FACTORS INDIVIDUALLY REFINED
Cross valid method: THROUGHOUT / ESU R: 0.618 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24024 804 5 %RANDOM
Rwork0.19629 ---
all0.19836 15304 --
obs0.19836 15304 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.308 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å21.39 Å2-0 Å2
2--2.78 Å2-0 Å2
3----4.17 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 0 2 98 3195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223164
X-RAY DIFFRACTIONr_bond_other_d0.0010.022157
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9524272
X-RAY DIFFRACTIONr_angle_other_deg0.70835306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.2495394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.39625.263114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.09115569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.822152
X-RAY DIFFRACTIONr_chiral_restr0.0750.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023449
X-RAY DIFFRACTIONr_gen_planes_other00.02617
X-RAY DIFFRACTIONr_mcbond_it0.6271.51965
X-RAY DIFFRACTIONr_mcbond_other0.11.5817
X-RAY DIFFRACTIONr_mcangle_it1.21823166
X-RAY DIFFRACTIONr_scbond_it1.82631199
X-RAY DIFFRACTIONr_scangle_it2.9884.51106
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 66 -
Rwork0.29 1091 -
obs-1091 99.83 %
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)
15.8686-5.74132.083712.985-7.099410.8783-0.25240.2170.2350.0459-0.1265-0.3925-0.6264-0.07960.3790.37270.0251-0.040.2483-0.17890.251135.742518.9796-23.7002
23.8045-1.9779-0.95784.19030.39285.483-0.3014-0.0495-0.36920.1351-0.05260.180.69190.04950.3540.1790.08660.01440.0955-0.06870.1336.796818.8735-1.4556
35.16745.1109-8.32279.2579-3.629918.6535-0.1064-0.7037-0.3760.1074-0.2913-0.50180.59561.34310.39770.37390.1905-0.10190.5985-0.10760.560347.795918.2269-0.7759
43.45411.2505-1.29023.9511-1.61115.6930.1181-0.0472-0.3529-0.0911-0.0007-0.09720.7561-0.095-0.11740.15530.027-0.10820.1154-0.05970.184629.228722.905818.584
514.1428-2.52-0.33510.63770.18476.65360.1745-1.46-0.72910.26170.010.07950.67160.3697-0.18450.5894-0.2286-0.11350.60170.05060.463433.903924.975529.8678
68.03251.2171-1.31654.9386-1.08472.65220.0863-0.2444-0.94260.2982-0.00320.22740.1466-0.1581-0.08310.0550.0128-0.0150.22160.06150.16918.745732.806819.6134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 82
2X-RAY DIFFRACTION2A83 - 177
3X-RAY DIFFRACTION3B48 - 72
4X-RAY DIFFRACTION4B73 - 177
5X-RAY DIFFRACTION5C42 - 78
6X-RAY DIFFRACTION6C79 - 177

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