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- PDB-4hw6: Crystal structure of an auxiliary nutrient binding protein (BACOV... -

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Basic information

Entry
Database: PDB / ID: 4hw6
TitleCrystal structure of an auxiliary nutrient binding protein (BACOVA_00264) from Bacteroides ovatus ATCC 8483 at 1.70 A resolution
Componentshypothetical protein, IPT/TIG domain protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / putative carbohydrate bindning two domains protein / IPT/TIG domain (PF01833) / 6-beta-propeller / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


TolB, C-terminal domain / IPT/TIG domain / ig-like, plexins, transcription factors / IPT domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins ...TolB, C-terminal domain / IPT/TIG domain / ig-like, plexins, transcription factors / IPT domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / IPT/TIG domain protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACOVA_00264) from Bacteroides ovatus ATCC 8483 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: 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 1.5Nov 20, 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, IPT/TIG domain protein
B: hypothetical protein, IPT/TIG domain protein
C: hypothetical protein, IPT/TIG domain protein
D: hypothetical protein, IPT/TIG domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,80641
Polymers196,9984
Non-polymers2,80837
Water35,5441973
1
A: hypothetical protein, IPT/TIG domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6428
Polymers49,2491
Non-polymers3937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: hypothetical protein, IPT/TIG domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,42516
Polymers49,2491
Non-polymers1,17515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: hypothetical protein, IPT/TIG domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9178
Polymers49,2491
Non-polymers6677
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: hypothetical protein, IPT/TIG domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8229
Polymers49,2491
Non-polymers5738
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.294, 81.554, 128.532
Angle α, β, γ (deg.)90.000, 108.600, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
hypothetical protein, IPT/TIG domain protein


Mass: 49249.457 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: ZP_02063319.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7LR39
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1973 / 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 34-465 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.0M magnesium chloride, 0.1M Sodium Iodide, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.918401, 0.979338
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 20, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9184011
20.9793381
ReflectionResolution: 1.7→29.894 Å / Num. all: 224161 / Num. obs: 224161 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rsym value: 0.106 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.743.70.9590.761439164890.95999.8
1.74-1.793.70.701160030160810.70199.9
1.79-1.843.70.5511.358171156110.55199.9
1.84-1.93.70.4191.756896152490.41999.9
1.9-1.963.70.3272.254834146930.327100
1.96-2.033.70.2572.853570143570.257100
2.03-2.113.70.2113.451251137530.211100
2.11-2.193.70.1694.349404132470.169100
2.19-2.293.70.149447460127410.149100
2.29-2.43.70.1235.945365121910.123100
2.4-2.533.70.1076.743178116110.107100
2.53-2.693.70.0947.640580109480.094100
2.69-2.873.70.0818.538012103050.081100
2.87-3.13.70.079.33539596090.07100
3.1-3.43.60.0610.33228288850.06100
3.4-3.83.60.05111.62858280010.051100
3.8-4.393.40.04513.52423270880.04599.9
4.39-5.383.70.03915.22196560130.03999.9
5.38-7.63.80.04314.91794746980.043100
7.6-29.8943.70.03716.7960925910.03798.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
REFMAC5.6.0117refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.894 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 3.267 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.084
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. IODIDE (IOD) IONS FROM THE CRYSTALLIZATION SOLUTION ARE MODELED AND ARE SUPPORTED BY THE ANOMALOUS DIFFERENCE FOURIERS. 7. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1789 11237 5 %RANDOM
Rwork0.1492 ---
obs0.1507 224086 99.87 %-
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: 149.9 Å2 / Biso mean: 28.5088 Å2 / Biso min: 10.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.25 Å2
2---0.41 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13447 0 82 1973 15502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214155
X-RAY DIFFRACTIONr_bond_other_d0.0010.029549
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.93219255
X-RAY DIFFRACTIONr_angle_other_deg0.831323128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37451787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59123.862725
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.129152257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1271592
X-RAY DIFFRACTIONr_chiral_restr0.0830.22008
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216189
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023139
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 814 -
Rwork0.256 15241 -
all-16055 -
obs--99.65 %
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)
110.0318-5.89473.18685.0135-2.76143.63440.13330.49760.1262-0.3951-0.1549-0.3810.35180.37080.02150.14820.02580.07460.385-0.00360.305767.06235.452109.394
27.0213-1.46480.21652.8883-1.02736.00210.0626-0.0125-0.30880.05790.1443-0.0950.1159-0.116-0.20690.03920.00310.00120.23300.186957.55135.938114.065
30.4684-0.07910.0760.86450.10810.81460.0058-0.0201-0.03210.03360.0099-0.08280.04740.0957-0.01560.01070.00430.00330.03710.00180.053326.63957.277135.48
49.84383.84512.09115.5244-0.24155.29160.3382-0.68970.24420.5754-0.3274-0.5059-0.40530.4792-0.01080.1857-0.0569-0.08780.4531-0.01940.25957.73735.839135.65
50.38190.0503-0.11661.12710.20720.38620.01460.0414-0.0256-0.1225-0.0215-0.0036-0.00720.00190.00690.03740.00990.01710.03720.00720.04828.29519.857101.702
60.7511-0.0572-0.06431.7970.4491.0755-0.0077-0.0294-0.07740.0997-0.02-0.02990.08050.05240.02760.02750.00710.02250.01830.01660.03828.5899.698115.555
75.98482.99823.69541.65291.73764.12250.17430.01440.080.0646-0.06090.00320.3537-0.1356-0.11340.25570.0893-0.13960.2361-0.05010.184771.49728.03588.366
80.6817-0.1341-0.00371.00120.06820.57150.01060.06320.0484-0.0272-0.0122-0.1121-0.03350.11540.00160.0617-0.0151-0.01320.08920.01510.04753.8696.66748.382
91.08280.08280.0661.82890.1420.92670.0287-0.1832-0.00610.2787-0.0637-0.09210.01530.10270.0350.1196-0.0301-0.01590.08220.01660.01449.1155.08865.059
108.3562-2.9287-2.35374.444-0.29628.14780.36490.53010.2709-0.01230.2768-0.85880.39971.4379-0.64170.10020.1359-0.08550.7718-0.28210.402582.28927.48666.02
119.721-3.3294-1.02013.9265-0.89158.24820.07220.20960.27790.20830.4894-0.60540.19590.8405-0.56160.09040.0889-0.06950.5852-0.18030.300477.63129.40368.889
120.5236-0.13570.06440.9215-0.22461.0713-0.00860.02870.0499-0.0287-0.0856-0.107-0.02210.11080.09420.0449-0.00680.00190.0520.03020.043141.48748.95979.422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 60
2X-RAY DIFFRACTION2A61 - 138
3X-RAY DIFFRACTION3A139 - 465
4X-RAY DIFFRACTION4B44 - 139
5X-RAY DIFFRACTION5B140 - 286
6X-RAY DIFFRACTION6B287 - 465
7X-RAY DIFFRACTION7C42 - 141
8X-RAY DIFFRACTION8C142 - 334
9X-RAY DIFFRACTION9C335 - 465
10X-RAY DIFFRACTION10D42 - 90
11X-RAY DIFFRACTION11D91 - 140
12X-RAY DIFFRACTION12D141 - 465

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