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- PDB-3hrp: Crystal structure of Structural genomics protein of unknown funct... -

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Basic information

Entry
Database: PDB / ID: 3hrp
TitleCrystal structure of Structural genomics protein of unknown function (NP_812590.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.70 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NP_812590.1 / Structural genomics protein of unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


TolB, C-terminal domain / IPT/TIG domain / IPT domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins ...TolB, C-terminal domain / IPT/TIG domain / IPT domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IPT/TIG domain-containing protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of Structural genomics protein of unknown function (NP_812590.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,26516
Polymers45,2781
Non-polymers98715
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.104, 84.915, 94.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY PROVIDES SUPPORTING EVIDENCE THAT THE MONOMER IS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION

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Components

#1: Protein Uncharacterized protein


Mass: 45277.516 Da / Num. of mol.: 1 / Fragment: sequence database residues 23-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3679, NP_812590.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A1I2
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 23-430 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: 2.26 Å3/Da / Density % sol: 45.58 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND .
Crystal growTemperature: 277 K / pH: 7.64
Details: 32.0000% 2-methyl-2,4-pentanediol, 0.2000M magnesium chloride, 0.1M Imidazole pH 7.64, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97889,0.97824
DetectorType: MAR MAR325 / Detector: CCD / Date: Feb 19, 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
20.978891
30.978241
ReflectionResolution: 1.7→29.49 Å / Num. obs: 45480 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.05 % / Biso Wilson estimate: 16.64 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.78
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 1.5 / % possible all: 93

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.49 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 5.164 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R: 0.105 / ESU R Free: 0.098
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. A MPD PLUS 15 EDO'S FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE STRUCTURE. 5. 8 N-TERMINAL RESIDUES WITHIN THE STRUCTURE ARE DISODERED. 6. ADDITIONAL DENSITY ADJACENT TO GLU76 WAS MODELED AS 2 WATERS BUT COULD ALSO BE DUE TO POSTTRANSLATIONAL MODIFICATION OF THAT RESIDUE.
RfactorNum. reflection% reflection
Rfree0.195 2293 5 %
Rwork0.169 --
obs0.17 45441 98.8 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20 Å2
2---0.73 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 64 354 3525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223363
X-RAY DIFFRACTIONr_bond_other_d0.0010.022295
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.964563
X-RAY DIFFRACTIONr_angle_other_deg0.77535612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84325154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9715556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4021514
X-RAY DIFFRACTIONr_chiral_restr0.0770.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023802
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02681
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_it0.5321.52049
X-RAY DIFFRACTIONr_mcbond_other0.1671.5850
X-RAY DIFFRACTIONr_mcangle_it0.8823326
X-RAY DIFFRACTIONr_scbond_it1.63731314
X-RAY DIFFRACTIONr_scangle_it2.4984.51222
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 177 -
Rwork0.257 3001 -
obs--95.06 %
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)
10.1171-0.40130.77321.9733-2.09976.0390.01260.01470.0071-0.0993-0.0599-0.0780.30040.30210.04740.05510.035-0.00010.16350.00680.112459.498-14.678-2.116
22.2025-0.6789-1.22610.96680.81163.0658-0.0921-0.13690.07960.13470.08910.0140.0390.12510.0030.04740.0243-0.00760.1149-0.01080.09652.221-8.9146.271
30.63090.16930.2372.14440.68311.4773-0.02910.0360.0296-0.39670.00070.036-0.23890.04240.02830.09080.0004-0.00640.05860.00140.038528.07911.91518.295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 47
2X-RAY DIFFRACTION2A48 - 125
3X-RAY DIFFRACTION3A126 - 430

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