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- PDB-3d4e: Crystal structure of putative beta-lactamase inhibitor protein (N... -

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Basic information

Entry
Database: PDB / ID: 3d4e
TitleCrystal structure of putative beta-lactamase inhibitor protein (NP_721579.1) from STREPTOCOCCUS MUTANS at 1.40 A resolution
Componentsputative beta-lactamase inhibitor protein
KeywordsHYDROLASE / NP_721579.1 / putative beta-lactamase inhibitor protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Unknown function
Function / homologyProtein of unknown function DUF3862 / Domain of Unknown Function with PDB structure (DUF3862) / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / BamE-like / 2-Layer Sandwich / Alpha Beta / ACETATE ION / Uncharacterized protein
Function and homology information
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative beta-lactamase inhibitor protein (NP_721579.1) from STREPTOCOCCUS MUTANS at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative beta-lactamase inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4005
Polymers20,1551
Non-polymers2454
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)180.695, 28.373, 32.640
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein putative beta-lactamase inhibitor protein


Mass: 20155.027 Da / Num. of mol.: 1 / Mutation: V150I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: Clarke [NCTC 10449]' / Gene: NP_721579.1, SMU_1196c / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8DTX1
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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. THE CLONED CONSTRUCT CONTAINS RESIDUES 29-206 OF THE TARGET SEQUENCE. THE STRAIN CLONED, STREPTOCOCCUS MUTANS CLARKE, DIFFERS FROM THE DATABASE STRAIN, STREPTOCOCCUS MUTANS UA159. SEQUENCING OF THE CLONED CONSTRUCT SHOWS AN ISOLUCINE AT POSITION 150 INSTEAD OF A VALINE. THE ISOLUCINE AT POSITION 150 IS SUPPORTED BY THE ELECTRON DENSITY.

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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: 40.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.0000M LiCl, 20.0000% PEG-6000, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97932,0.97916
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 16, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
30.979161
ReflectionResolution: 1.4→32.634 Å / Num. obs: 32922 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.262 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.4-1.450.5012.411443324498.8
1.45-1.510.3423.411778334499.2
1.51-1.580.2414.811677331599.3
1.58-1.660.1796.311168316099.9
1.66-1.760.1318.411114313799.6
1.76-1.90.08612.111971339299.6
1.9-2.090.05417.411476325399.6
2.09-2.390.04321.111645332599.6
2.39-3.010.03624.311760333399.6
3.010.02827.711712341998.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDAUTOSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→32.634 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.001 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.064
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.ACETATE ION FROM CRYSTALLIZATION AND ETHYLENE GLYCOL MOLECULES FROM CRYO CONDITION ARE MODELED IN THE STRUCTURE. 5.THERE IS A LONG REGION OF UNMODELED DENSITY NEAR RESIDUE 113 IN THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1667 5.1 %RANDOM
Rwork0.175 ---
obs0.176 32922 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.513 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20.44 Å2
2--1.29 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.4→32.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 16 157 1423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211400
X-RAY DIFFRACTIONr_bond_other_d0.0020.02921
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9431904
X-RAY DIFFRACTIONr_angle_other_deg1.41932266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2525186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63826.32468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.88415240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.04154
X-RAY DIFFRACTIONr_chiral_restr0.0970.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021653
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02276
X-RAY DIFFRACTIONr_mcbond_it1.7143882
X-RAY DIFFRACTIONr_mcbond_other0.4393357
X-RAY DIFFRACTIONr_mcangle_it2.79451427
X-RAY DIFFRACTIONr_scbond_it4.2148518
X-RAY DIFFRACTIONr_scangle_it6.49111477
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 119 -
Rwork0.272 2275 -
all-2394 -
obs--98.36 %
Refinement TLS params.Method: refined / Origin x: 66.6507 Å / Origin y: 23.0335 Å / Origin z: 12.3906 Å
111213212223313233
T-0.0302 Å2-0.0075 Å20.0035 Å2--0.0213 Å2-0.0141 Å2---0.0248 Å2
L1.1819 °2-0.4192 °2-0.1541 °2-0.9294 °20.0917 °2--0.4087 °2
S-0.059 Å °-0.0055 Å °0.0228 Å °-0.0122 Å °0.0814 Å °-0.1876 Å °0.0007 Å °0.0115 Å °-0.0225 Å °

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