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- PDB-6nlw: The crystal structure of class D carbapenem-hydrolyzing beta-lact... -

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Basic information

Entry
Database: PDB / ID: 6nlw
TitleThe crystal structure of class D carbapenem-hydrolyzing beta-lactamase BlaA from Shewanella oneidensis MR-1
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / 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
FORMIC ACID / MALONIC ACID / DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTan, K. / Tesar, C. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: The crystal structure of class D carbapenem-hydrolyzing beta-lactamase BlaA from Shewanella oneidensis MR-1
Authors: Tan, K. / Tesar, C. / Endres, M. / Joachimiak, A.
History
DepositionJan 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,41652
Polymers113,6204
Non-polymers3,79548
Water9,620534
1
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,92029
Polymers56,8102
Non-polymers2,11027
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-193 kcal/mol
Surface area19790 Å2
MethodPISA
2
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,49623
Polymers56,8102
Non-polymers1,68521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-180 kcal/mol
Surface area19970 Å2
MethodPISA
3
A: Beta-lactamase
C: Beta-lactamase
hetero molecules

A: Beta-lactamase
C: Beta-lactamase
hetero molecules

B: Beta-lactamase
hetero molecules

B: Beta-lactamase
hetero molecules

D: Beta-lactamase
hetero molecules

D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,831104
Polymers227,2418
Non-polymers7,59096
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation3_556x+1/2,y+1/2,z+11
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
crystal symmetry operation4_456-x-1/2,y+1/2,-z+11
Buried area24440 Å2
ΔGint-858 kcal/mol
Surface area80400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.333, 61.391, 122.802
Angle α, β, γ (deg.)90.00, 119.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-504-

HOH

21D-521-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase


Mass: 28405.115 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: blaOXA-54 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q6RFZ0, beta-lactamase

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Non-polymers , 7 types, 582 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 3.15M Ammonium Sulphate, 0.1M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 11, 2018 / Details: mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 96799 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 22.765 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.051 / Rrim(I) all: 0.111 / Χ2: 1.515 / Net I/σ(I): 21.39
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4811 / CC1/2: 0.733 / Rpim(I) all: 0.396 / Rrim(I) all: 0.85 / Χ2: 1.048 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OE0
Resolution: 1.85→39.029 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.91
RfactorNum. reflection% reflection
Rfree0.2251 4822 4.99 %
Rwork0.1833 --
obs0.1854 96641 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→39.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7913 0 207 534 8654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018295
X-RAY DIFFRACTIONf_angle_d0.9311232
X-RAY DIFFRACTIONf_dihedral_angle_d5.5715765
X-RAY DIFFRACTIONf_chiral_restr0.0631162
X-RAY DIFFRACTIONf_plane_restr0.0061426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.29261560.23773008X-RAY DIFFRACTION99
1.871-1.8930.2931440.22593044X-RAY DIFFRACTION100
1.893-1.91610.26211660.2113066X-RAY DIFFRACTION100
1.9161-1.94040.25281500.20563017X-RAY DIFFRACTION100
1.9404-1.96590.28221520.21473096X-RAY DIFFRACTION100
1.9659-1.99280.25351650.2113011X-RAY DIFFRACTION100
1.9928-2.02130.25831600.19453034X-RAY DIFFRACTION100
2.0213-2.05150.24351520.1883113X-RAY DIFFRACTION100
2.0515-2.08350.24331560.18432998X-RAY DIFFRACTION100
2.0835-2.11770.23461590.18443081X-RAY DIFFRACTION100
2.1177-2.15420.2431480.17843040X-RAY DIFFRACTION100
2.1542-2.19340.25621520.17693078X-RAY DIFFRACTION100
2.1934-2.23560.20591650.1742997X-RAY DIFFRACTION100
2.2356-2.28120.24031500.17023087X-RAY DIFFRACTION100
2.2812-2.33080.21631560.16433036X-RAY DIFFRACTION100
2.3308-2.3850.22671530.17833078X-RAY DIFFRACTION100
2.385-2.44460.21091720.18043038X-RAY DIFFRACTION100
2.4446-2.51070.26351550.1793040X-RAY DIFFRACTION100
2.5107-2.58460.22741700.17513068X-RAY DIFFRACTION100
2.5846-2.6680.23471710.18063057X-RAY DIFFRACTION100
2.668-2.76330.21751590.17793051X-RAY DIFFRACTION100
2.7633-2.87390.17861520.17333078X-RAY DIFFRACTION100
2.8739-3.00470.24461940.18243020X-RAY DIFFRACTION100
3.0047-3.1630.22021460.18523083X-RAY DIFFRACTION100
3.163-3.36110.20931610.17763082X-RAY DIFFRACTION100
3.3611-3.62040.22841450.16773109X-RAY DIFFRACTION100
3.6204-3.98440.18262050.16043027X-RAY DIFFRACTION100
3.9844-4.56020.21081580.16313107X-RAY DIFFRACTION100
4.5602-5.74250.20561510.18863138X-RAY DIFFRACTION100
5.7425-39.03790.25131990.23553137X-RAY DIFFRACTION99
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)
12.94290.1399-0.60375.758-1.11595.3012-0.0867-0.0591-0.17160.4942-0.1819-0.19110.2245-0.02840.23990.3048-0.01230.02310.3599-0.09450.2308-22.051-29.664432.7443
21.50890.4897-0.03378.34151.64392.847-0.0066-0.3158-0.00010.76510.0628-0.11680.40330.2591-0.03880.27360.0679-0.01260.2734-0.02090.1742-24.6121-35.397628.7465
31.29350.27321.47521.19581.4085.86270.0243-0.12180.10130.1177-0.0490.0329-0.1826-0.1233-0.00510.1840.030.01410.1646-0.01130.1716-38.4382-30.244119.814
41.4234-0.19060.16193.87520.23611.9923-0.13020.04080.2675-0.1861-0.11630.0598-0.4354-0.09070.2450.20840.0349-0.0670.1443-0.02860.1999-41.2097-23.89520.3121
52.8046-1.45760.79632.2931.53122.6892-0.4067-0.11860.37190.01750.1254-0.1313-0.33890.11260.24670.23570.0338-0.03570.135-0.03830.2234-34.5888-22.03963.1848
62.62070.56260.45664.3157-2.10694.219-0.012-0.0012-0.0389-0.01450.13750.41170.028-0.5938-0.15120.15810.06290.0110.2294-0.05790.2128-48.3887-30.425311.0442
71.0564-0.1312-0.24050.76430.75551.7109-0.0034-0.19840.04560.0590.0561-0.0321-0.11460.0551-0.05270.18120.0356-0.00390.1624-0.01130.1517-31.321-31.210918.2608
84.6933-2.55660.53621.5339-0.31156.5179-0.09731.04120.7327-0.5888-0.227-0.5193-0.35750.09550.23180.5336-0.10230.30650.43420.07280.5388-8.0156-27.4912-17.2291
93.73180.1896-0.61643.2788-0.65493.14270.04350.64550.2663-0.37630.0368-0.2893-0.55060.1792-0.14260.4401-0.03850.06880.2702-0.00120.1982-15.3233-30.5929-16.1961
102.94280.6042-1.18143.2229-1.18162.6632-0.0270.2921-0.1402-0.26490.0787-0.1694-0.00250.0339-0.02350.19220.0325-0.00470.1921-0.0650.1597-15.9037-47.3407-10.9102
114.8361-1.96081.00093.3473-0.17652.3256-0.2416-0.4309-0.29050.25120.22860.04-0.05230.0535-0.06880.2092-0.00460.01460.23590.0280.189-14.7702-55.94377.9267
124.8857-2.7626-0.22735.4492-0.46432.17270.0608-0.4636-0.05740.21930.1178-0.132-0.03570.2018-0.00620.1515-0.00020.0060.19810.00330.1809-13.9351-49.54457.6007
134.4565-0.25071.56834.08090.165.30890.0284-0.0125-0.5177-0.12260.12730.06110.3591-0.1592-0.1010.21360.0129-0.00130.1931-0.03130.2431-19.7191-58.5805-6.4047
141.6606-0.4841-0.28711.66670.64711.48670.08940.09160.1174-0.26950.056-0.1554-0.0810.2566-0.12610.17030.00050.0270.1826-0.03030.1536-15.9591-40.346-7.6582
155.52181.1232-0.14892.76921.05036.8628-0.46480.0781-0.266-0.36860.24480.24540.19260.1340.19070.42090.01570.01080.33680.00970.134-93.9752-34.889619.6034
163.58-0.155-0.12971.3203-2.85716.2411-0.27330.4961-0.177-0.8310.12970.03560.43210.06370.15350.3861-0.0405-0.00520.2761-0.03430.1805-91.5969-40.861925.9419
171.63050.4031.35641.58250.13852.9466-0.08290.20960.0152-0.1942-0.0067-0.1784-0.09480.30620.06740.137-0.02830.04420.19110.01140.2246-77.5464-29.697941.2997
183.88632.96592.00554.0716-0.67163.8064-0.1737-0.16540.385-0.1855-0.02830.4051-0.3258-0.03060.20270.1677-0.02570.01770.13550.03090.2558-82.3063-22.874648.6821
192.8466-0.54630.51126.10081.69452.2551-0.04530.0523-0.1145-0.14340.1341-0.73670.1280.5803-0.11450.19720.00680.07060.36750.10890.3374-68.6697-32.549442.9034
201.69170.3962-0.02891.2082-0.56642.3009-0.04040.266-0.0541-0.28970.0555-0.10380.01780.1272-0.01910.2156-0.02210.03120.1932-0.00140.1729-85.3422-34.261835.0052
215.67243.54583.9462.30232.08047.2205-0.4575-0.71290.59970.08620.0730.1759-0.903-0.34860.36560.52390.12560.120.309-0.04340.3978-109.8327-24.059368.656
222.2819-0.8339-1.12873.13591.29332.04710.0019-0.27380.0710.24780.08160.055-0.1246-0.0385-0.0830.2395-0.0181-0.02510.24950.04350.1222-102.3761-36.528567.2919
236.44771.04361.19862.03060.34892.0764-0.15260.2892-0.3888-0.06020.0923-0.0850.1368-0.06760.01990.27960.0265-0.02390.1994-0.02080.2291-101.629-56.810649.5578
245.0861.5492-0.72162.6294-0.16050.11870.06940.2748-0.04520.03910.0805-0.08180.05140.0092-0.10990.17850.0223-0.05340.1893-0.00330.1604-105.0934-50.200648.281
255.23940.07313.96584.52280.86137.24890.0752-0.1214-0.39330.20240.0275-0.29920.26090.0533-0.1270.201-0.0335-0.0160.17220.0680.2635-98.6226-56.779363.6083
261.65590.6816-0.7951.3842-0.93621.68490.1253-0.1652-0.05610.1953-0.0303-0.0370.0218-0.14-0.08580.1793-0.0332-0.02370.17780.03210.1533-100.315-40.899162.6277
278.92437.8732.12699.84881.89282.4371-0.0925-0.38660.4158-0.2956-0.18520.191-0.3975-0.30660.29210.25740.0760.03910.23360.01760.1979-108.3563-27.277657.645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 102 )
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 119 )
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 141 )
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 265 )
8X-RAY DIFFRACTION8chain 'B' and (resid 24 through 38 )
9X-RAY DIFFRACTION9chain 'B' and (resid 39 through 58 )
10X-RAY DIFFRACTION10chain 'B' and (resid 59 through 83 )
11X-RAY DIFFRACTION11chain 'B' and (resid 84 through 105 )
12X-RAY DIFFRACTION12chain 'B' and (resid 106 through 119 )
13X-RAY DIFFRACTION13chain 'B' and (resid 120 through 141 )
14X-RAY DIFFRACTION14chain 'B' and (resid 142 through 265 )
15X-RAY DIFFRACTION15chain 'C' and (resid 23 through 38 )
16X-RAY DIFFRACTION16chain 'C' and (resid 39 through 56 )
17X-RAY DIFFRACTION17chain 'C' and (resid 57 through 102 )
18X-RAY DIFFRACTION18chain 'C' and (resid 103 through 119 )
19X-RAY DIFFRACTION19chain 'C' and (resid 120 through 141 )
20X-RAY DIFFRACTION20chain 'C' and (resid 142 through 265 )
21X-RAY DIFFRACTION21chain 'D' and (resid 24 through 38 )
22X-RAY DIFFRACTION22chain 'D' and (resid 39 through 82 )
23X-RAY DIFFRACTION23chain 'D' and (resid 83 through 102 )
24X-RAY DIFFRACTION24chain 'D' and (resid 103 through 119 )
25X-RAY DIFFRACTION25chain 'D' and (resid 120 through 141 )
26X-RAY DIFFRACTION26chain 'D' and (resid 142 through 243 )
27X-RAY DIFFRACTION27chain 'D' and (resid 244 through 265 )

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