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- PDB-4l1n: Crystal structure of a putative conserved lipoprotein (NT01CX_115... -

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Basic information

Entry
Database: PDB / ID: 4l1n
TitleCrystal structure of a putative conserved lipoprotein (NT01CX_1156) from Clostridium novyi NT at 2.70 A resolution
ComponentsConserved lipoprotein, putative
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF15525 family protein / DUF4652 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyUncharacterised protein PF15525, DUF4652 / Protein of unknown function DUF4652 / Domain of unknown function (DUF4652) / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta / membrane / Conserved lipoprotein, putative
Function and homology information
Biological speciesClostridium novyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative conserved lipoprotein (NT01CX_1156) from Clostridium novyi NT at 2.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved lipoprotein, putative


Theoretical massNumber of molelcules
Total (without water)23,5971
Polymers23,5971
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.870, 146.870, 125.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Conserved lipoprotein, putative


Mass: 23597.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium novyi (bacteria) / Strain: NT / Gene: NT01CX_1156 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A0PXY7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (36-240) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (36-240) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 5.54 Å3/Da / Density % sol: 77.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.20000M lithium sulfate, 30.00000% polyethylene glycol 400, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.7→44.915 Å / Num. obs: 14440 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 81.523 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.41
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.7-2.771.85580107399.7
2.77-2.8525259101399.4
2.85-2.932.55216100899.9
2.93-3.023.6492996199.4
3.02-3.124.8479594699.1
3.12-3.235.7419891099.3
3.23-3.358.5439289199.3
3.35-3.4910.64550846100
3.49-3.6412.44413829100
3.64-3.8214.94067772100
3.82-4.0316.1386074299.9
4.03-4.2718.2366471799.7
4.27-4.5620.6321165898.9
4.56-4.9320.1274062299.5
4.93-5.421.2302857499.8
5.4-6.0420.42703527100
6.04-6.9721.5234546699.6
6.97-8.5423.6185639599.5
8.54-12.0827.1143431098.4
12.0828.485718097.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.7→44.915 Å / Cor.coef. Fo:Fc: 0.9128 / Cor.coef. Fo:Fc free: 0.9078 / Occupancy max: 1 / Occupancy min: 0.75 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. THE N-TERMINAL RESIDUES (36-79) ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2006 723 5.01 %RANDOM
Rwork0.1976 ---
obs0.1978 14439 99.58 %-
Displacement parametersBiso max: 160.57 Å2 / Biso mean: 66.3923 Å2 / Biso min: 33.28 Å2
Baniso -1Baniso -2Baniso -3
1-11.2929 Å20 Å20 Å2
2--11.2929 Å20 Å2
3----22.5858 Å2
Refine analyzeLuzzati coordinate error obs: 0.392 Å
Refinement stepCycle: LAST / Resolution: 2.7→44.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 0 10 1288
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d628SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes176HARMONIC5
X-RAY DIFFRACTIONt_it1297HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion171SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1312SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1297HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1745HARMONIC21.23
X-RAY DIFFRACTIONt_omega_torsion3.66
X-RAY DIFFRACTIONt_other_torsion3.35
LS refinement shellResolution: 2.7→2.92 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2919 156 5.31 %
Rwork0.247 2782 -
all0.2494 2938 -
obs--99.58 %
Refinement TLS params.Method: refined / Origin x: 20.9548 Å / Origin y: -11.6104 Å / Origin z: -18.5285 Å
111213212223313233
T-0.1293 Å20.0725 Å20.0829 Å2--0.0577 Å2-0.0608 Å2---0.0276 Å2
L4.7996 °2-1.2492 °2-0.9065 °2-1.7628 °20.7359 °2--1.8728 °2
S0.0925 Å °0.399 Å °-0.1983 Å °-0.3694 Å °-0.1202 Å °-0.3728 Å °0.1834 Å °0.3186 Å °0.0277 Å °
Refinement TLS groupSelection details: {A|80 - 240}

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