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- PDB-3due: CRYSTAL STRUCTURE OF A PUTATIVE PERIPLASMIC PROTEIN FROM DUF2874 ... -

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Basic information

Entry
Database: PDB / ID: 3due
TitleCRYSTAL STRUCTURE OF A PUTATIVE PERIPLASMIC PROTEIN FROM DUF2874 FAMILY (BVU_2987) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.85 A RESOLUTION
ComponentsPutative periplasmic protein
KeywordsUNKNOWN FUNCTION / PUTATIVE PERIPLASMIC PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyInhibitor of vertebrate lysozyme, Ivy - #30 / Putative beta-lactamase-inhibitor-like, PepSY-like / Putative beta-lactamase-inhibitor-like, PepSY-like / Inhibitor of vertebrate lysozyme, Ivy / 3-Layer(aba) Sandwich / Alpha Beta / CACODYLATE ION / Putative periplasmic protein
Function and homology information
Biological speciesBacteroides vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function.
Authors: Das, D. / Finn, R.D. / Carlton, D. / Miller, M.D. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Chen, C. / Chiu, H.J. / Chiu, M. / Clayton, T. / Deller, M.C. / Duan, L. / ...Authors: Das, D. / Finn, R.D. / Carlton, D. / Miller, M.D. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Chen, C. / Chiu, H.J. / Chiu, M. / Clayton, T. / Deller, M.C. / Duan, L. / Ellrott, K. / Ernst, D. / Farr, C.L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Kumar, A. / Marciano, D. / McMullan, D. / Morse, A.T. / Nigoghossian, E. / Nopakun, A. / Okach, L. / Puckett, C. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Wooten, T. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJul 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 1.4Feb 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 1.5Oct 9, 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: Putative periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0262
Polymers14,8891
Non-polymers1371
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.601, 50.874, 79.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative periplasmic protein


Mass: 14889.206 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria)
Gene: YP_001300247.1, BVU_2987 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6L4L1
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 20-145) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 20-145) 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: 42.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 35.0000% 2-ethoxyethanol, 0.1M Cacodylate pH 6.5, 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: 0.91837,0.97926,0.97876
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 15, 2008 / 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
20.979261
30.978761
ReflectionResolution: 1.85→29.361 Å / Num. obs: 11519 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.91 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 5.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.85-1.93.60.5881.30.5881100
1.9-1.953.60.4471.70.4471100
1.95-2.013.60.3820.381100
2.01-2.073.60.2942.60.2941100
2.07-2.143.60.25530.2551100
2.14-2.213.60.2223.40.2221100
2.21-2.293.60.2033.50.2031100
2.29-2.393.60.1754.30.1751100
2.39-2.493.60.1674.50.1671100
2.49-2.623.60.1355.40.1351100
2.62-2.763.60.1285.30.1281100
2.76-2.933.60.1096.30.1091100
2.93-3.133.50.0966.90.0961100
3.13-3.383.50.07780.0771100
3.38-3.73.50.06680.0661100
3.7-4.143.50.05211.80.0521100
4.14-4.783.40.05710.50.0571100
4.78-5.853.40.0698.50.0691100
5.85-8.273.20.06410.30.0641100
8.27-29.372.80.05210.90.052197.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→29.361 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.13 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.144
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORAT 4. THE CACODYLATE MOLECULE WAS MODELED BASED ON CRYSTALLIZATION CONDITIONS AND IS SUPPORTED BY AN ANOMALOUS DIFFERENCE FOURIER MAP CALCULATED AT THIS WAVELENGTH.
RfactorNum. reflection% reflectionSelection details
Rfree0.23321 549 4.8 %RANDOM
Rwork0.19234 ---
obs0.19432 10931 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.076 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--0.68 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1019 0 5 133 1157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221070
X-RAY DIFFRACTIONr_bond_other_d0.0010.02693
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.9341460
X-RAY DIFFRACTIONr_angle_other_deg0.9431710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3675132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16826.36455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.8815180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.69151
X-RAY DIFFRACTIONr_chiral_restr0.1060.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021199
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02203
X-RAY DIFFRACTIONr_nbd_refined0.2120.2192
X-RAY DIFFRACTIONr_nbd_other0.1930.2667
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2519
X-RAY DIFFRACTIONr_nbtor_other0.0890.2512
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3350.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4222665
X-RAY DIFFRACTIONr_mcbond_other0.3432254
X-RAY DIFFRACTIONr_mcangle_it1.96431056
X-RAY DIFFRACTIONr_scbond_it1.5022475
X-RAY DIFFRACTIONr_scangle_it2.2373401
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 40 -
Rwork0.218 789 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 9.6413 Å / Origin y: 49.8873 Å / Origin z: 7.6608 Å
111213212223313233
T-0.1253 Å20.0031 Å20.034 Å2--0.1413 Å20.0117 Å2---0.1046 Å2
L1.4798 °20.0635 °20.2355 °2-0.9561 °20.1531 °2--2.9269 °2
S0.0455 Å °-0.1466 Å °-0.015 Å °0.1258 Å °-0.0034 Å °0.0475 Å °0.0682 Å °0.0335 Å °-0.0421 Å °

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