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- PDB-3bww: Crystal structure of a duf692 family protein (hs_1138) from haemo... -

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Basic information

Entry
Database: PDB / ID: 3bww
TitleCrystal structure of a duf692 family protein (hs_1138) from haemophilus somnus 129pt at 2.20 A resolution
ComponentsProtein of unknown function DUF692/COG3220
KeywordsMETAL BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Uncharacterised protein family UPF0276 / RiPP precursor modification enzyme MbnB/TglH/ChrH / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / : / Uncharacterized protein
Similarity search - Component
Biological speciesHaemophilus somnus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function (DUF692/COG3220) (YP_719350.1) from Haemophilus somnus 129PT at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein of unknown function DUF692/COG3220
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9636
Polymers35,5901
Non-polymers3735
Water2,216123
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.572, 65.992, 95.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein of unknown function DUF692/COG3220


Mass: 35590.387 Da / Num. of mol.: 1 / Fragment: Residues 62-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus somnus (bacteria) / Species: Histophilus somni / Strain: 129PT / Gene: YP_719350.1, HS_1138 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q0I408
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.33
Details: NANODROP, 7.5% PEG 8000, 34.0% 2-methyl-2,4-pentanediol, 0.1M Sodium cacodylate pH 6.33, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91840, 0.97939, 0.97953
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.979391
30.979531
ReflectionResolution: 2.2→28.689 Å / Num. obs: 17792 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 34.907 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.263.60.60.7456712850.6100
2.26-2.323.70.7311465612650.731100
2.32-2.393.70.4611.5450112140.461100
2.39-2.463.70.3821.8444412030.382100
2.46-2.543.70.3412.1429811620.341100
2.54-2.633.70.2722.6413311210.272100
2.63-2.733.70.2213.2398510870.221100
2.73-2.843.60.1883.7384210530.188100
2.84-2.973.70.1534.6369510040.153100
2.97-3.113.70.1295.234739500.129100
3.11-3.283.70.1076.234149290.107100
3.28-3.483.60.0877.231688760.087100
3.48-3.723.60.0836.829008140.083100
3.72-4.023.60.078.827507720.07100
4.02-4.43.60.05610.825927260.056100
4.4-4.923.50.0571022796440.05799.9
4.92-5.683.50.0677.420325800.06799.7
5.68-6.963.40.0767.816924930.07699.4
6.96-9.843.40.0578.913383920.05798.7
9.84-28.6893.10.0745.66852220.07494

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.2→28.689 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.907 / SU B: 17.664 / SU ML: 0.206 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.214
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. THE PRESENCE OF IRON AND ARSENIC WERE CONFIRMED BY X-RAY FLUORESCENCE. THE METAL IDENTITY AT THE INDIVIDUAL FE AND CACODYLATE ION SITES WAS BASED ON ANOMALOUS DIFFERENCE FOURIER MAP COMPARISONS WITH DATA COLLECTED ABOVE AND BELOW THE FOLLOWING K ABSORPTION EDGES: FE, ZN, AS AND SE.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 883 5.1 %RANDOM
Rwork0.195 ---
obs0.198 17291 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.101 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20 Å2
2--1.72 Å20 Å2
3----2.98 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 15 123 2124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222092
X-RAY DIFFRACTIONr_bond_other_d0.0020.021379
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9582843
X-RAY DIFFRACTIONr_angle_other_deg1.0133371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4715261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28524.47996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66215348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8121510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
X-RAY DIFFRACTIONr_nbd_refined0.20.2416
X-RAY DIFFRACTIONr_nbd_other0.1870.21394
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2987
X-RAY DIFFRACTIONr_nbtor_other0.0890.21089
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.289
X-RAY DIFFRACTIONr_metal_ion_refined0.2780.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3230.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.23
X-RAY DIFFRACTIONr_mcbond_it0.8181.51338
X-RAY DIFFRACTIONr_mcbond_other0.1471.5520
X-RAY DIFFRACTIONr_mcangle_it1.4522086
X-RAY DIFFRACTIONr_scbond_it2.1433863
X-RAY DIFFRACTIONr_scangle_it3.1094.5757
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.591 42 -
Rwork0.452 924 -
all-966 -
obs--75.23 %
Refinement TLS params.Method: refined / Origin x: 34.6318 Å / Origin y: 40.609 Å / Origin z: 15.4131 Å
111213212223313233
T-0.1547 Å20.0492 Å20.0167 Å2--0.191 Å20.0362 Å2---0.1752 Å2
L0.9469 °20.299 °20.2255 °2-1.2623 °2-0.514 °2--4.2166 °2
S0.0621 Å °-0.1299 Å °-0.111 Å °0.1259 Å °0.0217 Å °0.0099 Å °0.164 Å °0.0284 Å °-0.0838 Å °

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