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- PDB-3gmu: Crystal Structure of Beta-Lactamse Inhibitory Protein (BLIP) in A... -

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Basic information

Entry
Database: PDB / ID: 3gmu
TitleCrystal Structure of Beta-Lactamse Inhibitory Protein (BLIP) in Apo Form
ComponentsBeta-lactamase inhibitory protein
KeywordsPROTEIN BINDING / 2-layer alpha/beta sandwich / Disulfide bond / Secreted
Function / homology
Function and homology information


regulation of beta-lactamase activity / extracellular region
Similarity search - Function
Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / BamE-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / Beta-lactamase inhibitory protein
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsStrynadka, N.C.J. / Gretes, M. / James, M.N.G.
Citation
Journal: 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.
#1: Journal: Nature / Year: 1994
Title: Structural and kinetic characterization of a beta-lactamase-inhibitor protein.
Authors: Strynadka, N.C. / Jensen, S.E. / Johns, K. / Blanchard, H. / Page, M. / Matagne, A. / Frere, J.M. / James, M.N.
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 20, 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
B: Beta-lactamase inhibitory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6713
Polymers17,5561
Non-polymers1142
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.650, 26.190, 48.070
Angle α, β, γ (deg.)90.000, 113.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-281-

HOH

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Components

#1: Protein Beta-lactamase inhibitory protein / BLIP


Mass: 17556.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell culture filtrate / Source: (natural) Streptomyces clavuligerus (bacteria) / Strain: NRRL 3585 / References: UniProt: P35804
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 10 mg/ml protein, 20% saturated ammonium sulfate, 50 mM sodium citrate, pH 5.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54056 Å
DetectorType: SDMS TWIN AREA DETECTOR SYSTEM / Detector: AREA DETECTOR / Date: Dec 17, 1992
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.98→59.34 Å / Num. obs: 9038 / % possible obs: 84.6 % / Redundancy: 1.9 % / Rsym value: 0.178 / Net I/σ(I): 7.4
Reflection shellResolution: 1.98→2.03 Å / Mean I/σ(I) obs: 1.8 / % possible all: 64.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å14.37 Å
Translation2.5 Å14.37 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→59.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.149 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.863 / SU B: 3.915 / SU ML: 0.115 / SU R Cruickshank DPI: 0.228 / SU Rfree: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 429 4.7 %RANDOM
Rwork0.164 ---
obs0.167 9038 84.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.93 Å2 / Biso mean: 18.946 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20.35 Å2
2---0.04 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.98→59.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 6 114 1361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221273
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.9251732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61723.88954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35315186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.586155
X-RAY DIFFRACTIONr_chiral_restr0.1260.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02984
X-RAY DIFFRACTIONr_nbd_refined0.2010.2510
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2900
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.214
X-RAY DIFFRACTIONr_mcbond_it1.2811.5829
X-RAY DIFFRACTIONr_mcangle_it2.10821291
X-RAY DIFFRACTIONr_scbond_it3.3683519
X-RAY DIFFRACTIONr_scangle_it4.7734.5440
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 11 -
Rwork0.161 231 -
all-242 -
obs--29.88 %

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