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- PDB-4nlm: 1.18 Angstrom resolution crystal structure of uncharacterized pro... -

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Basic information

Entry
Database: PDB / ID: 4nlm
Title1.18 Angstrom resolution crystal structure of uncharacterized protein lmo1340 from Listeria monocytogenes EGD-e
ComponentsLmo1340 protein
KeywordsStructural genomics / Unknown function / Surface proteins / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology: / YqgU-like 6-bladed beta propeller domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lmo1340 protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.18 Å
AuthorsHalavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.18 Angstrom resolution crystal structure of uncharacterized protein lmo1340 from Listeria monocytogenes EGD-e
Authors: Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lmo1340 protein


Theoretical massNumber of molelcules
Total (without water)42,2231
Polymers42,2231
Non-polymers00
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.224, 69.990, 52.905
Angle α, β, γ (deg.)90.00, 95.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lmo1340 protein


Mass: 42223.316 Da / Num. of mol.: 1 / Fragment: UNP residues 25-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: lmo1340 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q8Y7E3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: protein - 7.5 mg/mL in 10 mM Tris-HCl, pH 8.3, 0.5 M NaCl 5 mM BME, Crystallization - The PACT Suite (#D2: 0.1 M MMT buffer pH 5, 25 % (w/v) PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 21, 2012 / Details: Be lenses
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.18→30 Å / Num. all: 112400 / Num. obs: 112400 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 31.7
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.33 / Num. unique all: 5714 / % possible all: 97.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
MLPHAREphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.18→24.21 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.535 / SU ML: 0.031 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18116 5628 5 %RANDOM
Rwork0.14503 ---
obs0.14678 106618 95.86 %-
all-106618 --
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 19.499 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å2-0.02 Å2
2--2.4 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 1.18→24.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 0 499 3169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023003
X-RAY DIFFRACTIONr_bond_other_d0.0010.022828
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9664107
X-RAY DIFFRACTIONr_angle_other_deg0.71836561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8865381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28525.625144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.11715531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.941159
X-RAY DIFFRACTIONr_chiral_restr0.0960.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023516
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02695
X-RAY DIFFRACTIONr_rigid_bond_restr12.87235831
X-RAY DIFFRACTIONr_sphericity_free37.1787104
X-RAY DIFFRACTIONr_sphericity_bonded15.3676156
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 427 -
Rwork0.227 8018 -
obs-8018 97.94 %

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