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- PDB-3h3i: CRYSTAL STRUCTURE OF A PUTATIVE LIPID BINDING PROTEIN (BT_2261) F... -

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Basic information

Entry
Database: PDB / ID: 3h3i
TitleCRYSTAL STRUCTURE OF A PUTATIVE LIPID BINDING PROTEIN (BT_2261) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.20 A RESOLUTION
ComponentsPutative lipid binding protein
KeywordsLIPID BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyLipocalin - #220 / Lipid-binding, putative / Lipid-binding superfamily / Lipid-binding putative hydrolase / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta / Lipid-binding hydrolase
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of Putative lipid binding protein (NP_811174.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative lipid binding protein
B: Putative lipid binding protein
C: Putative lipid binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9519
Polymers50,3753
Non-polymers5766
Water3,675204
1
A: Putative lipid binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8882
Polymers16,7921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative lipid binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9843
Polymers16,7921
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative lipid binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0804
Polymers16,7921
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.383, 67.383, 186.164
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 6 / Auth seq-ID: 29 - 166 / Label seq-ID: 13 - 150

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein Putative lipid binding protein


Mass: 16791.572 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_2261, NP_811174.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A5H8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CLONED CONSTRUCT INCLUDING RESIDUES 18-166 WAS EXPRESSED WITH A PURIFICATION TAG ...THE CLONED CONSTRUCT INCLUDING RESIDUES 18-166 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5000M (NH4)2SO4, 1.0000M Li2SO4, 0.1M Citrate pH 5.6, 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: 0.91837,0.97895,0.97833
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 23, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978951
30.978331
ReflectionResolution: 2.2→29.604 Å / Num. obs: 25038 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 39.658 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 7.078
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.267.50.591.21380618450.59100
2.26-2.327.60.4851.51340417710.485100
2.32-2.397.50.3861.91316117500.386100
2.39-2.467.50.3432.21241716510.343100
2.46-2.547.50.2912.61233216340.291100
2.54-2.637.50.2263.31203816060.226100
2.63-2.737.50.1993.71147115210.199100
2.73-2.847.50.1574.81109514840.157100
2.84-2.977.50.1325.61060814060.132100
2.97-3.117.50.1036.91016813600.103100
3.11-3.287.50.097.3963712840.09100
3.28-3.487.40.0768.8921412390.076100
3.48-3.727.50.0628.8872411670.062100
3.72-4.027.50.05611.8796610660.056100
4.02-4.47.40.04713.573369920.047100
4.4-4.927.40.0451466909050.045100
4.92-5.687.30.04713.459448110.047100
5.68-6.967.20.05511.449866910.055100
6.96-9.846.90.0531237795440.053100
9.84-29.616.20.04612.919373110.04696.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.604 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 12.824 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.2
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.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.SULFATES (SO4) FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1272 5.1 %RANDOM
Rwork0.187 ---
obs0.189 24985 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.49 Å2 / Biso mean: 19.713 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.34 Å20 Å2
2--0.69 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 30 204 3443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223356
X-RAY DIFFRACTIONr_bond_other_d0.0010.022098
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9294590
X-RAY DIFFRACTIONr_angle_other_deg0.84935117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6695425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.21625.244164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.54615491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.815159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023846
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02715
X-RAY DIFFRACTIONr_mcbond_it0.87122070
X-RAY DIFFRACTIONr_mcbond_other0.1552853
X-RAY DIFFRACTIONr_mcangle_it1.74943332
X-RAY DIFFRACTIONr_scbond_it3.261286
X-RAY DIFFRACTIONr_scangle_it4.53481251
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1680 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.215
BLOOSE POSITIONAL0.225
CLOOSE POSITIONAL0.265
ALOOSE THERMAL2.7710
BLOOSE THERMAL1.910
CLOOSE THERMAL2.0610
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 89 -
Rwork0.244 1747 -
all-1836 -
obs--99.78 %
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)
11.86780.74530.4872.76730.73873.00740.28240.0743-0.283-0.00090.012-0.07380.95910.7168-0.29440.38880.3075-0.16210.2827-0.13610.221211.68760.530850.0551
22.95430.35190.67641.8570.88583.42740.1030.02790.27080.3842-0.10250.12550.918-0.1845-0.00050.3907-0.1238-0.00180.0655-0.04150.1588-15.449463.007329.6397
35.24661.76710.30751.72950.09764.3333-0.0443-0.29480.2062-0.1993-0.0135-0.026-0.3722-0.6730.05780.07550.05050.03240.1424-0.0570.1496-18.926786.860353.5985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 166
2X-RAY DIFFRACTION2B29 - 166
3X-RAY DIFFRACTION3C29 - 166

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