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- PDB-4g5a: Crystal structure of a putative member of duf 3244 protein family... -

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Basic information

Entry
Database: PDB / ID: 4g5a
TitleCrystal structure of a putative member of duf 3244 protein family (BT_1867) from Bacteroides thetaiotaomicron VPI-5482 at 1.69 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Immunoglobulin - like beta-sandwich / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyImmunoglobulin-like - #3080 / Protein of unknown function DUF3244 / Domain of unknown function (DUF3244) / Immunoglobulin-like / Sandwich / Mainly Beta / DUF3244 domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.69 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative member of duf 3244 protein family (BT_1867) from Bacteroides thetaiotaomicron VPI-5482 at 1.69 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 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 1.3Nov 20, 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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0604
Polymers22,8762
Non-polymers1842
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-27 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.042, 93.255, 27.654
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 0 - 121 / Label seq-ID: 1 - 99

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 11437.938 Da / Num. of mol.: 2 / Fragment: UNP residues 24-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_1867 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8A6L2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 24-121 OF 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.095M sodium citrate pH 5.6, 19% 2-propanol, 5% glycerol, 19% polyethylene glycol 4000, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97949,0.97882
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2012
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
20.979491
30.978821
ReflectionResolution: 1.69→27.704 Å / Num. obs: 25699 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.931 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.047 / Net I/σ(I): 13.99 / Num. measured all: 90460
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.69-1.750.7360.4581.99035482846530.61196.4
1.75-1.820.840.3082.88690488045790.41393.8
1.82-1.90.9340.194.39157474746590.25398.1
1.9-20.9680.1246.79338487347190.16596.8
2-2.130.9850.0849.59319508447920.11294.3
2.13-2.290.990.06312.18619474944650.08494
2.29-2.520.9940.0514.99484489847750.06697.5
2.52-2.890.9970.03619.98797491245840.04793.3
2.89-3.630.9980.02230.39239484346130.0395.3
3.630.9990.01738.48782494245070.02291.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.69→27.704 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.099 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.102
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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) GLYCEROL(GOL) FROM THE CRYSTALLIZATION BUFFER HAS BEEN MODELED INTO THE STRUCTURE. 3). ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4). THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES. 5). WATERS WERE EXCLUDED FROM TLS REFINEMENT. 6) HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 1309 5.1 %RANDOM
Rwork0.1776 ---
obs0.1791 24351 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.268 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2--0.29 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.69→27.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 12 200 1816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221797
X-RAY DIFFRACTIONr_bond_other_d0.0010.021199
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9652479
X-RAY DIFFRACTIONr_angle_other_deg0.84932982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6865244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26925.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.815322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.38154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02352
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.77831066
X-RAY DIFFRACTIONr_mcbond_other0.6063422
X-RAY DIFFRACTIONr_mcangle_it3.14451774
X-RAY DIFFRACTIONr_scbond_it4.6528731
X-RAY DIFFRACTIONr_scangle_it7.44911683
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1263 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.480.5
medium thermal0.852
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 86 -
Rwork0.252 1806 -
obs--99.06 %
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)
10.10920.40620.06670.74030.11250.1725-0.0064-0.07640.0142-0.1054-0.0269-0.04810.0684-0.01510.03340.0362-0.0094-0.00230.0089-0.00050.019765.91962.11690.4834
20.99470.3990.19460.13790.00470.0877-0.0351-0.1332-0.0787-0.08630.0006-0.0101-0.01070.02480.03450.0018-0.0107-0.00150.03490.00790.025983.535916.11261.7008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 121
2X-RAY DIFFRACTION2B0 - 121

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