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- PDB-4y0t: Crystal structure of apo form of OXA-58, a Carbapenem hydrolyzing... -

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Basic information

Entry
Database: PDB / ID: 4y0t
TitleCrystal structure of apo form of OXA-58, a Carbapenem hydrolyzing Class D beta-lactamase from Acinetobacter baumanii (P21, 4mol/ASU)
ComponentsBeta-lactamase
KeywordsHYDROLASE / Class D beta-lactamase / OXA-58 / 4mol/ASU
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsPratap, S. / Katiki, M. / Gill, P. / Golemi-Kotra, D. / Kumar, P.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2015
Title: Active-Site Plasticity Is Essential to Carbapenem Hydrolysis by OXA-58 Class D beta-Lactamase of Acinetobacter baumannii.
Authors: Pratap, S. / Katiki, M. / Gill, P. / Kumar, P. / Golemi-Kotra, D.
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)125,9934
Polymers125,9934
Non-polymers00
Water6,990388
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)31,4981
Polymers31,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)31,4981
Polymers31,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)31,4981
Polymers31,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)31,4981
Polymers31,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.017, 65.095, 191.964
Angle α, β, γ (deg.)90.00, 91.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A38 - 86
2010D38 - 86
1020A87 - 279
2020D87 - 279

NCS ensembles :
ID
1
2

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Components

#1: Protein
Beta-lactamase /


Mass: 31498.209 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaOXA-58, bla-oxa-58, bla-oxa58 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2TR58, beta-lactamase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 32.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris base/Hydrochloric acid (pH 8.0) and 28% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.29→34.79 Å / Num. obs: 37470 / % possible obs: 91.23 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.15
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.42 / % possible all: 74.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.3→34.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 20.364 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.765 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24328 1847 4.9 %RANDOM
Rwork0.19414 ---
obs0.19651 35622 91.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.466 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.54 Å2
2--0.87 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7740 0 0 388 8128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197934
X-RAY DIFFRACTIONr_bond_other_d0.0080.027601
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.94710720
X-RAY DIFFRACTIONr_angle_other_deg1.349317462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64824.883383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.764151370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1441536
X-RAY DIFFRACTIONr_chiral_restr0.0860.21151
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029016
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021880
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1891.8933868
X-RAY DIFFRACTIONr_mcbond_other1.1881.8933867
X-RAY DIFFRACTIONr_mcangle_it1.9842.8364825
X-RAY DIFFRACTIONr_mcangle_other1.9842.8364826
X-RAY DIFFRACTIONr_scbond_it1.3342.0074066
X-RAY DIFFRACTIONr_scbond_other1.3342.0074067
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2292.9545893
X-RAY DIFFRACTIONr_long_range_B_refined4.93615.4149128
X-RAY DIFFRACTIONr_long_range_B_other4.90615.249063
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2460 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2D
LS refinement shellResolution: 2.296→2.355 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 84 -
Rwork0.305 1837 -
obs--63.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.6606-0.69611.3281.6075-0.97223.940.0301-0.02810.20710.1664-0.0654-0.063-0.06980.22540.03530.049-0.0180.0510.33090.00220.1095-3.11.30374.161
24.83261.3668-0.68638.03970.94214.61390.09410.1894-0.52760.00420.00630.06170.5876-0.0052-0.10040.12760.0172-0.00440.4463-0.00930.1286-14.85-7.62753.66
32.1453-0.4770.39231.9704-1.39792.91140.07290.02390.0351-0.02160.00390.00160.0245-0.075-0.07680.0154-0.0190.00040.396-0.01990.0611-8.3050.94569.313
47.91823.9912.22894.4199-0.036511.49890.02320.3205-0.2254-0.2917-0.0271-0.52310.11960.00280.0040.2130.03210.0160.40850.0110.2075-59.67156.79237.616
54.53761.2367-1.66672.2627-0.73233.1015-0.19790.1216-0.1951-0.13840.0883-0.2880.0510.33810.10970.04290.04330.00410.37290.00410.1168-59.64553.16924.206
62.4084-0.72240.13560.84311.13592.4107-0.14070.2069-0.03610.1193-0.0390.1030.1416-0.26730.17970.1347-0.02820.02720.5629-0.01080.0173-43.14856.6575.629
77.13614.35752.61848.65240.50183.5679-0.3768-0.5631.14150.567-0.3198-0.3662-0.6117-0.20710.69660.22080.0819-0.15870.4668-0.00450.5624-42.65374.044.202
82.7678-0.5086-0.93853.28170.62132.0029-0.1832-0.14110.02740.0870.057-0.0650.03260.08870.12620.10960.004-0.0150.3755-0.01090.0211-47.84657.7613.658
94.0104-1.687-2.432.7775-0.51327.1661-0.1462-0.20220.30160.24790.0146-0.2745-0.1350.28330.13160.0677-0.004-0.03640.35490.00520.0943-56.76457.4036.345
109.0772-0.2117-3.68923.14040.83116.8845-0.23670.1907-0.35920.1322-0.06560.03150.5032-0.15020.30220.1624-0.03410.00890.3221-0.01670.0405-41.92748.33414.493
115.55580.4761-0.78232.4724-0.81340.4522-0.14430.24260.24250.09040.11380.088-0.0827-0.05970.03050.104-0.0043-0.01110.37430.01710.1187-46.2860.18620.803
123.43362.2518-1.00536.72141.37383.4327-0.3598-0.17680.1771-0.41430.0953-0.1772-0.5220.05690.26440.18440.0323-0.09680.36760.06720.1554-54.03961.18323.523
136.10013.69365.43493.62641.00668.7213-0.45770.12080.3591-0.31240.17590.1369-0.4417-0.10260.28170.12720.08010.10770.50320.08290.2608-49.93861.46131.926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 101
2X-RAY DIFFRACTION2A102 - 141
3X-RAY DIFFRACTION3A142 - 279
4X-RAY DIFFRACTION4D38 - 50
5X-RAY DIFFRACTION5D51 - 81
6X-RAY DIFFRACTION6D82 - 101
7X-RAY DIFFRACTION7D102 - 121
8X-RAY DIFFRACTION8D122 - 161
9X-RAY DIFFRACTION9D162 - 181
10X-RAY DIFFRACTION10D182 - 201
11X-RAY DIFFRACTION11D202 - 241
12X-RAY DIFFRACTION12D242 - 261
13X-RAY DIFFRACTION13D262 - 279

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