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- PDB-3gmv: Crystal Structure of Beta-Lactamse Inhibitory Protein-I (BLIP-I) ... -

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Basic information

Entry
Database: PDB / ID: 3gmv
TitleCrystal Structure of Beta-Lactamse Inhibitory Protein-I (BLIP-I) in Apo Form
ComponentsBeta-lactamase inhibitory protein BLIP-I
KeywordsPROTEIN BINDING / 2-layer alpha/beta sandwich
Function / homologyBLIP domain / Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Beta-lactamase inhibitory protein BLIP-I precusor
Function and homology information
Biological speciesStreptomyces exfoliatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLim, D.C. / Gretes, M. / Strynadka, N.C.J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Insights into positive and negative requirements for protein-protein interactions by crystallographic analysis of the beta-lactamase inhibitory proteins BLIP, BLIP-I, and BLP.
Authors: Gretes, M. / Lim, D.C. / de Castro, L. / Jensen, S.E. / Kang, S.G. / Lee, K.J. / Strynadka, N.C.
History
DepositionMar 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
X: Beta-lactamase inhibitory protein BLIP-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3822
Polymers17,2191
Non-polymers1631
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.735, 44.071, 45.291
Angle α, β, γ (deg.)90.00, 104.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase inhibitory protein BLIP-I


Mass: 17218.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces exfoliatus (bacteria) / Strain: SMF19 / Gene: bliA / Plasmid: pET30a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9KJ90
#2: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 294 K / Method: hanging drop vapor batch
Details: 20 mg/ml protein in 50 mM tris, pH 8.0, 50 mM NaCl mixed 1:1 with well solution 30% PEG 4000, 0.3 M lithium chloride, 0.1 M TrisCl, pH 8.5, hanging drop vapor batch, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 13, 2000
RadiationMonochromator: DOUBLE CRYSTAL SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 17522 / % possible obs: 91 % / Rsym value: 0.041 / Net I/σ(I): 28.336
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 11.6 / Rsym value: 0.094 / % possible all: 68.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20.49 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.053 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22695 795 4.8 %RANDOM
Rwork0.18543 ---
obs0.1874 15645 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å20.23 Å2
2--0.6 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 0 11 201 1433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221270
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9491725
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.995157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81724.23759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10515188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.107154
X-RAY DIFFRACTIONr_chiral_restr0.1110.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021995
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.2591
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2872
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8521.5777
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49721237
X-RAY DIFFRACTIONr_scbond_it2.3913493
X-RAY DIFFRACTIONr_scangle_it3.8834.5487
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 48 -
Rwork0.211 1087 -
obs--100 %

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