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- PDB-4kh8: Crystal structure of a Lipocalin-like protein (EF0376) from Enter... -

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Basic information

Entry
Database: PDB / ID: 4kh8
TitleCrystal structure of a Lipocalin-like protein (EF0376) from Enterococcus faecalis V583 at 1.60 A resolution
Componentshypothetical protein
KeywordsStructural Genomics / Unknown Function / Lipocalin-like fold / two domains / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF4822 / Domain of unknown function DUF4822 / Domain of unknown function (DUF4822) / Lipocalin / Beta Barrel / Mainly Beta / Unknown ligand / DUF4822 domain-containing protein
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (EF0376) from Enterococcus faecalis V583 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.5Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0559
Polymers36,3831
Non-polymers6728
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.745, 99.745, 56.956
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein hypothetical protein


Mass: 36382.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_0376, NP_814167.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q838Q9
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 31-347) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 31-347) 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12.0% Glycerol, 1.5M ammonium sulfate, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97903,0.97871
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979031
30.978711
ReflectionResolution: 1.6→27.046 Å / Num. all: 42670 / Num. obs: 42670 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rsym value: 0.121 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.646.40.6811.12007431600.681100
1.64-1.696.30.5941.31931430630.594100
1.69-1.746.20.4971.51837529730.49799.9
1.74-1.795.60.3951.91615128820.39599.8
1.79-1.856.10.3232.31709928060.32399.9
1.85-1.916.50.2672.81762427180.267100
1.91-1.986.40.2083.61656226060.208100
1.98-2.076.20.174.31554725270.17100
2.07-2.165.70.1375.41368724220.13799.9
2.16-2.266.20.1295.71433323190.12999.9
2.26-2.396.50.1196.11431722050.119100
2.39-2.536.40.116.61332420780.11100
2.53-2.76.20.0947.51224419720.09499.9
2.7-2.925.70.0759.21049318290.07599.9
2.92-3.26.70.0728.81130216940.07299.9
3.2-3.586.50.0678.4989915240.06799.7
3.58-4.135.60.0687.9753113440.06899.3
4.13-5.066.40.0747.2736111490.07499.9
5.06-7.166.20.086.955729030.0899.7
7.16-27.0465.90.0737.929344960.07398.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→27.046 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.5 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.076
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2 .A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2 .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. 4.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.6.SULFATES (SO4) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1727 2150 5 %RANDOM
Rwork0.1408 ---
obs0.1424 42647 99.84 %-
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 max: 97.07 Å2 / Biso mean: 16.6849 Å2 / Biso min: 6.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.03 Å20 Å2
2---0.03 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2501 0 40 351 2892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022627
X-RAY DIFFRACTIONr_bond_other_d0.0010.022337
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9533570
X-RAY DIFFRACTIONr_angle_other_deg0.78335376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6485324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26724.967153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.50815420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7691518
X-RAY DIFFRACTIONr_chiral_restr0.0950.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02660
X-RAY DIFFRACTIONr_mcbond_it1.5631.7311257
X-RAY DIFFRACTIONr_mcbond_other1.5631.731256
X-RAY DIFFRACTIONr_mcangle_it2.2873.2411573
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 138 -
Rwork0.195 3008 -
all-3146 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 64.3537 Å / Origin y: -0.3752 Å / Origin z: -3.4174 Å
111213212223313233
T0.0254 Å20.0015 Å20.0026 Å2-0.0293 Å2-0.0038 Å2--0.0108 Å2
L0.3343 °20.0553 °20.0348 °2-0.824 °20.0278 °2--0.1246 °2
S-0.0018 Å °0.017 Å °0.0002 Å °-0.0382 Å °0.0137 Å °-0.0669 Å °-0.0027 Å °0.0297 Å °-0.0119 Å °

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