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- PDB-5c0u: Crystal structure of the copper-bound form of MerB mutant D99S -

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Basic information

Entry
Database: PDB / ID: 5c0u
TitleCrystal structure of the copper-bound form of MerB mutant D99S
ComponentsAlkylmercury lyase
KeywordsLYASE / METAL BINDING PROTEIN / Bacterial Proteins / Cysteine / Escherichia coli / Lyases / copper / Mutation
Function / homology
Function and homology information


alkylmercury lyase / alkylmercury lyase activity / organomercury catabolic process / response to mercury ion
Similarity search - Function
Beta-Lactamase - #410 / Alkylmercury lyase, helix-turn-helix domain / Helix-turn-helix domain of alkylmercury lyase / Alkylmercury lyase / Alkylmercury lyase / Beta-Lactamase / Winged helix DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / COPPER (II) ION / Alkylmercury lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsWahba, H.M. / Lecoq, L. / Stevenson, M. / Mansour, A. / Cappadocia, L. / Lafrance-Vanasse, J. / Wilkinson, K.J. / Sygusch, J. / Wilcox, D.E. / Omichinski, J.G.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
National Science Foundation (NSF, United States) United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage ...Title: Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity.
Authors: Wahba, H.M. / Lecoq, L. / Stevenson, M. / Mansour, A. / Cappadocia, L. / Lafrance-Vanasse, J. / Wilkinson, K.J. / Sygusch, J. / Wilcox, D.E. / Omichinski, J.G.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Feb 24, 2016Group: Database references
Revision 1.3Mar 2, 2016Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkylmercury lyase
B: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2685
Polymers46,0612
Non-polymers2073
Water5,801322
1
A: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1743
Polymers23,0301
Non-polymers1432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0942
Polymers23,0301
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.903, 88.958, 52.005
Angle α, β, γ (deg.)90.000, 100.640, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 208
211chain BB1 - 208

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Components

#1: Protein Alkylmercury lyase / / Organomercurial lyase


Mass: 23030.258 Da / Num. of mol.: 2 / Mutation: D99S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: merB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77072, alkylmercury lyase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 1.87 Å3/Da / Density % sol: 34.25 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23 % polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide. Before flash freezing, the same precipitant was used except 25 % polyethylene glycol 2000 MME was ...Details: 23 % polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide. Before flash freezing, the same precipitant was used except 25 % polyethylene glycol 2000 MME was used as a cryo-protectant.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.376 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.376 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Number: 86858 / Rmerge(I) obs: 0.052 / Χ2: 1.36 / D res high: 1.87 Å / D res low: 50 Å / Num. obs: 25316 / % possible obs: 90.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.075010.0382.0423.5
4.035.0710.0382.1863.4
3.524.0310.0442.2733.5
3.23.5210.0472.1413.5
2.973.210.051.9653.4
2.792.9710.0551.7343.5
2.652.7910.0581.6063.5
2.542.6510.0611.5543.5
2.442.5410.0661.4543.4
2.362.4410.0661.2493.3
2.282.3610.0691.1863.4
2.222.2810.0711.1383.4
2.162.2210.0811.0643.5
2.112.1610.0830.9213.4
2.062.1110.0890.8943.4
2.012.0610.0990.8863.4
1.972.0110.10.6563.4
1.941.9710.1170.6613.4
1.91.9410.1270.5523.5
1.871.910.1430.563.3
ReflectionResolution: 1.87→50 Å / Num. obs: 25316 / % possible obs: 90.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.32 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Χ2: 1.357 / Net I/av σ(I): 28.475 / Net I/σ(I): 12.5 / Num. measured all: 86858
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.87-1.93.30.14310390.9720.0910.170.5674.3
1.9-1.943.50.12712520.9760.080.150.55290.4
1.94-1.973.40.11713120.9790.0740.1390.66194.1
1.97-2.013.40.113200.9840.0640.120.65692.7
2.01-2.063.40.09912580.9830.0620.1170.88692.2
2.06-2.113.40.08912400.9870.0550.1050.89488.3
2.11-2.163.40.08311530.9860.0530.0990.92183.4
2.16-2.223.50.08112850.9880.050.0951.06491.9
2.22-2.283.40.07113210.9890.0450.0851.13895.1
2.28-2.363.40.06913130.990.0440.0821.18692.9
2.36-2.443.30.06612730.9910.0430.0791.24992.8
2.44-2.543.40.06612580.9890.0420.0791.45487.8
2.54-2.653.50.06111980.9930.0380.0721.55487.2
2.65-2.793.50.05813330.9890.0360.0681.60695.1
2.79-2.973.50.05513190.9940.0340.0651.73494.4
2.97-3.23.40.0512870.9940.0310.0591.96591.7
3.2-3.523.50.04712250.9950.0290.0552.14187.5
3.52-4.033.50.04413470.9950.0270.0512.27394.9
4.03-5.073.40.03812360.9960.0240.0452.18688
5.07-503.50.03813470.9970.0230.0452.04293

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F0O
Resolution: 1.87→31.071 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1918 3841 7.98 %
Rwork0.147 44309 -
obs0.1507 48150 87.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.13 Å2 / Biso mean: 27.5082 Å2 / Biso min: 6.53 Å2
Refinement stepCycle: final / Resolution: 1.87→31.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 3 322 3499
Biso mean--27 34.38 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093279
X-RAY DIFFRACTIONf_angle_d1.2334465
X-RAY DIFFRACTIONf_chiral_restr0.06527
X-RAY DIFFRACTIONf_plane_restr0.007574
X-RAY DIFFRACTIONf_dihedral_angle_d12.561167
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1726X-RAY DIFFRACTION7.835TORSIONAL
12B1726X-RAY DIFFRACTION7.835TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8702-1.89390.27921070.21861231X-RAY DIFFRACTION65
1.8939-1.91880.22941330.19331538X-RAY DIFFRACTION84
1.9188-1.94510.21821460.16231709X-RAY DIFFRACTION89
1.9451-1.97290.21181470.1541704X-RAY DIFFRACTION90
1.9729-2.00230.21741430.16031661X-RAY DIFFRACTION88
2.0023-2.03360.21171450.1481670X-RAY DIFFRACTION90
2.0336-2.06690.19991420.15481652X-RAY DIFFRACTION87
2.0669-2.10260.20111430.15461641X-RAY DIFFRACTION85
2.1026-2.14080.21691280.15281513X-RAY DIFFRACTION83
2.1408-2.1820.2531320.15691500X-RAY DIFFRACTION79
2.182-2.22650.19911460.15021727X-RAY DIFFRACTION91
2.2265-2.27490.23561450.15411676X-RAY DIFFRACTION91
2.2749-2.32780.19971500.15591724X-RAY DIFFRACTION91
2.3278-2.3860.23191460.15731701X-RAY DIFFRACTION90
2.386-2.45050.22151410.15071610X-RAY DIFFRACTION87
2.4505-2.52250.24511420.17461647X-RAY DIFFRACTION86
2.5225-2.60390.25391230.16891433X-RAY DIFFRACTION77
2.6039-2.69690.19291540.15261770X-RAY DIFFRACTION93
2.6969-2.80490.23781540.15871736X-RAY DIFFRACTION94
2.8049-2.93240.171540.14571751X-RAY DIFFRACTION92
2.9324-3.08690.20161460.13811652X-RAY DIFFRACTION89
3.0869-3.28010.14221360.14351561X-RAY DIFFRACTION84
3.2801-3.5330.1891510.13981707X-RAY DIFFRACTION90
3.533-3.8880.15371510.13311780X-RAY DIFFRACTION94
3.888-4.44920.16591510.12381704X-RAY DIFFRACTION91
4.4492-5.60010.16131360.12951622X-RAY DIFFRACTION86
5.6001-31.07530.15591490.14121689X-RAY DIFFRACTION90
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)
13.76510.23220.21674.4559-1.39013.2163-0.05640.015-0.0098-0.09790.0825-0.15780.0314-0.21660.00990.15380.00780.09250.2528-0.00660.2358-0.92323.93241.5014
21.0861-0.1239-0.16682.5059-0.66191.7158-0.4219-0.0846-0.13611.12390.23670.11640.38570.05780.07190.54870.06480.03180.105-0.04380.215712.6637-14.676337.831
30.99030.2596-0.00840.8698-0.54711.9788-0.29940.03280.28370.8091-0.29181.13270.4358-0.376-0.03120.3105-0.03950.23350.122-0.17920.34656.2969-17.353630.7781
40.6416-0.0030.33852.89370.0641.1545-0.04660.1215-0.1149-0.035-0.0341-0.1350.07330.14570.09620.11510.0135-0.0070.0987-0.0150.095115.7181-4.002726.9795
52.0027-0.71160.07642.0095-0.21072.3239-0.0353-0.0508-0.09970.0736-0.02940.16980.09-0.14110.04020.081-0.0084-0.00030.0682-0.020.07628.27787.47333.3775
63.21510.5310.72642.92520.51972.976-0.3027-0.6679-0.34-0.19550.22830.44950.12280.16770.08890.230.03450.06280.32160.12340.21654.80713.15930.4773
73.01080.694-1.09233.68850.15474.28450.21260.3283-0.1294-0.586-0.4151-0.1324-0.08180.20580.1370.19820.0726-0.02260.22990.07380.18313.312-15.13425.6547
82.0727-0.7607-0.21632.76110.51512.56930.28270.26350.1615-0.2723-0.1541-0.22960.0680.1198-0.0670.10150.03180.00570.13460.03470.17348.1086-20.072311.5795
91.0656-1.06190.22882.8777-0.22341.1397-0.074-0.0097-0.09160.15040.07120.2013-0.0043-0.1583-0.02150.1030.0290.00720.15980.02860.1065-4.6458-10.151117.3769
101.4599-0.012-0.30432.9640.75031.53110.07910.08050.05280.071-0.12190.30360.1075-0.12410.05270.08920.0284-0.00580.1620.01820.1161-11.9479-1.836410.7908
113.9685-1.8640.06742.96340.33881.5845-0.0364-0.1002-0.34890.0029-0.0613-0.9834-0.07050.666-0.03110.13810.00290.08510.40530.05180.40076.60364.20788.2425
122.0572-0.2454-0.15491.70420.07192.1946-0.00960.07010.249-0.131-0.0884-0.1903-0.05760.34740.05990.12470.0131-0.01440.24750.07080.1288-1.48184.63137.594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 49 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 69 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 96 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 208 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 14 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 15 through 33 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 34 through 69 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 70 through 96 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 97 through 141 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 142 through 153 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 154 through 208 )B0

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