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- PDB-3hlz: Crystal structure of BT_1490 (NP_810393.1) from BACTEROIDES THETA... -

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Basic information

Entry
Database: PDB / ID: 3hlz
TitleCrystal structure of BT_1490 (NP_810393.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.50 A resolution
Componentsuncharacterized protein BT_1490
Keywordsstructural genomics / unknown function / NP_810393.1 / BT_1490 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Four Helix Bundle (Hemerythrin (Met), subunit A) - #1090 / Domain of unknown function DUF3806 / Domain of unknown function DUF3805 / Domain of unknown function (DUF3805) / Domain of unknown function (DUF3806) / Mog1/PsbP, alpha/beta/alpha sandwich / Protein Transport Mog1p; Chain A / Mog1/PsbP, alpha/beta/alpha sandwich / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1090 / Domain of unknown function DUF3806 / Domain of unknown function DUF3805 / Domain of unknown function (DUF3805) / Domain of unknown function (DUF3806) / Mog1/PsbP, alpha/beta/alpha sandwich / Protein Transport Mog1p; Chain A / Mog1/PsbP, alpha/beta/alpha sandwich / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of BT_1490 (NP_810393.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein BT_1490
B: uncharacterized protein BT_1490
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,89211
Polymers61,2472
Non-polymers6459
Water8,071448
1
A: uncharacterized protein BT_1490
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0186
Polymers30,6241
Non-polymers3945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein BT_1490
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8745
Polymers30,6241
Non-polymers2504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.210, 62.087, 68.555
Angle α, β, γ (deg.)90.390, 91.500, 97.340
Int Tables number1
Space group name H-MP1

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Components

#1: Protein uncharacterized protein BT_1490


Mass: 30623.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1480, NP_810393.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A7P4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE THE CONSTRUCT (RESIDUES 23-178) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...SEQUENCE THE CONSTRUCT (RESIDUES 23-178) 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2000M Ca(OAc)2, 20.0000% PEG-8000, 0.1M MES pH 6.0, 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: 0.91837,0.97845
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 16, 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
20.978451
ReflectionResolution: 1.5→29.814 Å / Num. obs: 76979 / % possible obs: 87.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.871 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.550.3041.41271110843170.3
1.55-1.620.2091.91808915473184.6
1.62-1.690.1692.51536113179185.6
1.69-1.780.133.41663414340186.8
1.78-1.890.094.91636614178188.1
1.89-2.040.0547.81713614954189.4
2.04-2.240.03711.41653114504190.9
2.24-2.560.02914.81679614885192
2.56-3.230.02320.11730115524194.1
3.23-29.8140.018281719615790196.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.814 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.953 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.078
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 0.85 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4 GLYCEROL (GOL), ACETATE (ACT), AND CALCIUM (CA) FROM THE CRYSTALLIZATION/CRYOGEN SOLUTIONS WERE MODELED INTO THE STRUCTURE. 4. UN-ASSIGNED ELECTRON DENSITES NEAR THE SIDECHAINS OF GLU 177 AND GLU 213 ON THE A SUBUNIT, AND LYS A73 ON THE A SUBUNIT WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 3838 5 %RANDOM
Rwork0.169 ---
obs0.171 76816 94 %-
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: 97.76 Å2 / Biso mean: 24.816 Å2 / Biso min: 11.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0.03 Å2-0.6 Å2
2---1.35 Å2-0.18 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4205 0 41 448 4694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224508
X-RAY DIFFRACTIONr_bond_other_d0.0010.023022
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9456146
X-RAY DIFFRACTIONr_angle_other_deg0.86837424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4285590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18625.607214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41715757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2841512
X-RAY DIFFRACTIONr_chiral_restr0.090.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025133
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02901
X-RAY DIFFRACTIONr_nbd_refined0.2360.2858
X-RAY DIFFRACTIONr_nbd_other0.1940.23055
X-RAY DIFFRACTIONr_nbtor_refined0.1880.22202
X-RAY DIFFRACTIONr_nbtor_other0.0850.22313
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2391
X-RAY DIFFRACTIONr_metal_ion_refined0.110.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3330.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.228
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0150.21
X-RAY DIFFRACTIONr_mcbond_it1.48522854
X-RAY DIFFRACTIONr_mcbond_other0.38221125
X-RAY DIFFRACTIONr_mcangle_it2.07634450
X-RAY DIFFRACTIONr_scbond_it1.70921987
X-RAY DIFFRACTIONr_scangle_it2.56631668
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 212 -
Rwork0.238 4224 -
all-4436 -
obs--73.9 %
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)
10.563-0.43680.01671.1765-0.23291.87750.0212-0.02430.04240.04060.0221-0.0545-0.0753-0.0465-0.0433-0.1277-0.01760.0208-0.09560.0025-0.118516.62764.5620.578
20.6443-0.74240.39023.548-1.23981.2248-0.0170.0832-0.017-0.1142-0.0469-0.17430.03820.0970.0639-0.1448-0.01340.0221-0.0702-0.0261-0.071230.22834.3535.72
30.7557-0.2596-0.1020.75010.0681.37080.0279-0.0271-0.06090.03010.02260.01390.07030.036-0.0506-0.1156-0.01780.0062-0.0984-0.0031-0.109117.46445.232-33.718
40.5862-0.45270.01362.87180.92661.11860.01220.05920.0481-0.0571-0.01580.094-0.0489-0.07570.0035-0.1489-0.01320.0289-0.07680.0199-0.1073.50675.151-29.03
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 131
2X-RAY DIFFRACTION2A132 - 268
3X-RAY DIFFRACTION3B0 - 131
4X-RAY DIFFRACTION4B132 - 268

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