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- PDB-3gmx: Crystal Structure of Beta-Lactamse Inhibitory Protein-Like Protei... -

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Basic information

Entry
Database: PDB / ID: 3gmx
TitleCrystal Structure of Beta-Lactamse Inhibitory Protein-Like Protein (BLP) at 1.05 Angstrom Resolution
ComponentsBLP
KeywordsPROTEIN BINDING / 2-layer alpha/beta sandwich
Function / homology
Function and homology information


BLIP 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
Similarity search - Domain/homology
ACETATE ION / Beta-Lactamase Inhibitory Protein-Like Protein / Beta-Lactamase Inhibitory Protein-Like Protein
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.05 Å
AuthorsGretes, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 27, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

Deposited unit
B: BLP
A: BLP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3416
Polymers35,1052
Non-polymers2364
Water14,124784
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-10 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.771, 99.925, 41.643
Angle α, β, γ (deg.)90.000, 101.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BLP


Mass: 17552.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Strain: ATCC 27064 / Gene: blp / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P97062, UniProt: B5GLC0*PLUS
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 294 K / Method: microbatch under oil / pH: 6.5
Details: starting concentration as follows: 5.5 mg/ml protein, 10% PEG 8000, 0.1 M magnesium acetate tetrahydrate, 50 mM sodium cacodylate, 75 mM NaCl, 15 mM tris, pH 6.5, microbatch under oil, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Feb 28, 2006
RadiationMonochromator: DOUBLE FLAT CRYSTAL SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 1.05→49.94 Å / Num. obs: 114297 / % possible obs: 86.1 % / Redundancy: 9.9 % / Rsym value: 0.06 / Χ2: 0.997 / Net I/σ(I): 6.5
Reflection shellResolution: 1.05→1.077 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5662 / Χ2: 1.084 / % possible all: 65.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å55.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→49.9 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.687 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.154 5754 5 %RANDOM
Rwork0.125 ---
obs0.126 114227 85.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.16 Å2 / Biso mean: 11.089 Å2 / Biso min: 2.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.2 Å2
2--0.01 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.05→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 16 784 3447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222763
X-RAY DIFFRACTIONr_bond_other_d0.0050.023
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9383788
X-RAY DIFFRACTIONr_angle_other_deg0.60736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5785352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62923.958144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43815435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1211519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022269
X-RAY DIFFRACTIONr_nbd_refined0.2070.21407
X-RAY DIFFRACTIONr_nbd_other0.3860.22
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2595
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.280
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4180.25
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.2121
X-RAY DIFFRACTIONr_mcbond_it1.3891.51708
X-RAY DIFFRACTIONr_mcangle_it1.98422718
X-RAY DIFFRACTIONr_scbond_it2.52831209
X-RAY DIFFRACTIONr_scangle_it3.1614.51061
X-RAY DIFFRACTIONr_rigid_bond_restr1.35932920
X-RAY DIFFRACTIONr_sphericity_free6.0693784
X-RAY DIFFRACTIONr_sphericity_bonded4.04632665
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 332 -
Rwork0.187 5908 -
all-6240 -
obs--65.9 %

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