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- PDB-4fur: Crystal Structure of Urease subunit gamma 2 from Brucella meliten... -

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Basic information

Entry
Database: PDB / ID: 4fur
TitleCrystal Structure of Urease subunit gamma 2 from Brucella melitensis biovar Abortus 2308
ComponentsUrease subunit gamma 2
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Urease
Function / homology
Function and homology information


urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease; subunit A / Urease, gamma-like subunit / Urease, gamma subunit / Urease, gamma/gamma-beta subunit / Urease, gamma subunit superfamily / Urease, gamma subunit / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Urease subunit gamma 2
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Urease subunit gamma 2 from Brucella melitensis biovar Abortus 2308
Authors: Fairman, J.W. / Davies, D.R. / Staker, B.L. / Stewart, L.
History
DepositionJun 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Urease subunit gamma 2
B: Urease subunit gamma 2
C: Urease subunit gamma 2
D: Urease subunit gamma 2
E: Urease subunit gamma 2
F: Urease subunit gamma 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,06520
Polymers67,5426
Non-polymers52314
Water6,882382
1
A: Urease subunit gamma 2
B: Urease subunit gamma 2
C: Urease subunit gamma 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9849
Polymers33,7713
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-27 kcal/mol
Surface area15400 Å2
MethodPISA
2
D: Urease subunit gamma 2
E: Urease subunit gamma 2
F: Urease subunit gamma 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,08111
Polymers33,7713
Non-polymers3108
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-31 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.510, 145.010, 137.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Urease subunit gamma 2 / Urea amidohydrolase subunit gamma 2


Mass: 11257.007 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus (bacteria)
Strain: 2308 / Gene: ureA2, BAB1_1376 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YQE0, urease
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus B2: 0.1 M Imidazole/MES pH 6.50, 0.09 M sodium fluoride, 0.09 M sodium bromide, 0.09 M sodium iodide, 30% ethylene glycol, 30% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.665
111/2H+1/2K, 3/2H-1/2K, -L20.173
11-1/2H+1/2K, 3/2H+1/2K, -L30.163
ReflectionResolution: 2.1→50 Å / Num. all: 48876 / Num. obs: 48192 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.178 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.150.3544.3713926321990.5
2.15-2.210.3565.2118236342197.9
2.21-2.280.3315.817887332698.4
2.28-2.350.315.9117977326298.7
2.35-2.420.2586.917395315098.9
2.42-2.510.2187.9817004307799.1
2.51-2.60.1759.4616471298499.3
2.6-2.710.15810.4615632284699.4
2.71-2.830.12912.0815251275499.6
2.83-2.970.11512.9814611264699.6
2.97-3.130.09215.3913856250799.8
3.13-3.320.07318.6413223238799.7
3.32-3.550.0622.8912267224799.8
3.55-3.830.052811513212699.8
3.83-4.20.04332.2910302193699.7
4.2-4.70.03935.819295175399.8
4.7-5.420.04730.88421156899.9
5.42-6.640.05227.8771471338100
6.64-9.390.03637.885303105299.7
9.390.0344.37278259395.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KAU
Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.491 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 2374 4.9 %RANDOM
Rwork0.1509 ---
all0.1527 48876 --
obs0.1527 48192 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.95 Å2 / Biso mean: 30.876 Å2 / Biso min: 3.75 Å2
Baniso -1Baniso -2Baniso -3
1--16 Å2-0 Å2-0 Å2
2---19.81 Å2-0 Å2
3---35.81 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4493 0 17 382 4892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194778
X-RAY DIFFRACTIONr_angle_refined_deg1.4442.0026526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6835652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.64225.179195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85415876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9591527
X-RAY DIFFRACTIONr_chiral_restr0.0830.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213551
LS refinement shellResolution: 2.1→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 152 -
Rwork0.171 2779 -
all-2931 -
obs--81.39 %
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)
110.4659-0.69070.67736.6965-1.57369.4982-0.3534-1.0575-0.1931.11240.34340.4216-0.1773-0.50480.010.38260.0230.03910.33530.02030.2106-4.05363.917423.5253
26.5561.1623-1.26243.2649-0.19151.3270.01460.39240.1052-0.28810.17080.1072-0.03990.0104-0.18540.09660.0097-0.0120.1259-0.03960.1049.964563.877211
34.7827-2.9925-1.54973.6516-0.09111.14720.19720.3434-0.5143-0.324-0.36330.22020.02330.00760.16610.18-0.0043-0.01210.2264-0.14110.4135-2.200752.54110.1858
410.4964-0.0366-8.54292.72121.268628.2047-0.51420.2342-0.6865-0.1309-0.11660.46650.8796-0.00110.63080.09530.0069-0.05580.0358-0.11390.4212.427745.30868.5124
54.6892-0.08472.37726.50.70416.16640.06110.3855-0.2197-0.5442-0.1245-0.08360.21150.16380.06350.0810.01880.03980.1306-0.1110.151817.70454.32848.6351
613.7660.1234-0.54121.08950.54840.3049-0.0759-0.0487-0.14030.28050.01030.14710.15420.00310.06560.10460.00180.00320.1870.02730.29542.084750.022918.3642
710.51621.4022-5.21686.4821-0.87674.67350.1920.1281-0.8312-0.14460.07230.36390.3216-0.182-0.26420.134-0.0114-0.12840.1336-0.02040.36259.034247.61314.6001
86.9185-2.86973.75737.4696-7.162322.36940.0967-1.0536-0.61250.22910.31670.03551.2628-0.1791-0.41340.3048-0.0086-0.07010.26390.0630.21279.964270.239222.6536
98.0266-2.27043.24444.9871-3.10096.88480.3870.0139-0.541-0.34210.03140.07190.437-0.0142-0.41840.1171-0.0023-0.04410.0799-0.01470.11893.819677.59611.1991
103.9814-1.94710.93632.8495-0.37190.36260.08910.22560.0379-0.1493-0.0463-0.1204-0.05880.0278-0.04280.1312-0.011-0.00670.1180.01960.07446.031383.980210.181
110.5472-1.2713-0.006219.6519-4.15281.07960.1466-0.04640.1155-0.5107-0.211-0.38760.01420.15260.06440.1106-0.02470.04560.19430.0130.237522.290581.40478.7521
123.79870.3961-1.15054.61071.03176.0308-0.11770.30410.2689-0.30130.08450.0282-0.27920.05420.03320.1132-0.02530.00020.10010.05010.08666.264393.89788.9482
134.0291-6.31450.260612.1033-0.29871.1637-0.0058-0.2208-0.03650.0261-0.0722-0.40430.01890.23640.0780.13860.015-0.04060.19150.04490.240719.980681.53818.1351
142.67011.3712-0.73535.4718-0.04982.0483-0.01420.1990.22330.19820.0181-0.6545-0.03970.4052-0.00380.1587-0.033-0.00830.18670.01210.193418.050289.281614.5723
150.6374-1.36210.04644.39992.72727.1777-0.1237-0.11120.34290.58820.0839-0.7069-0.07790.62710.03990.5149-0.1779-0.04650.6729-0.05120.3601-1.612379.463823.5842
160.86010.6113-0.3126.2511.68261.9832-0.02760.0690.0081-0.15540.1274-0.1907-0.04980.0933-0.09980.0724-0.01440.00120.1539-0.01210.0655-9.402367.98110.9176
173.9454-1.5566-0.63821.70550.90220.5116-0.19550.6152-0.1665-0.25490.04430.3235-0.11680.08640.15120.2607-0.0401-0.08010.26470.0570.2692-12.201584.893510.6281
188.4182-0.1515-1.04929.2256-5.632420.6057-0.12780.23210.17810.1735-0.19450.6967-0.4793-0.87950.32230.08110.0008-0.05340.15040.02790.2195-21.661482.95958.9111
193.85730.4455-1.00698.1002-1.5736.6386-0.04930.4327-0.1562-0.6102-0.02620.2299-0.0397-0.2370.07550.0957-0.0141-0.06690.1636-0.02720.0735-20.194965.67877.0916
200.88810.4368-1.48047.2635.85958.6805-0.0983-0.00570.1935-0.33620.26650.2796-0.18830.1859-0.16820.1280.0255-0.01510.2312-0.00890.1251-23.245667.320116.7044
214.26212.63361.49076.19360.19321.71020.1065-0.12440.28550.4896-0.08310.1396-0.1476-0.0245-0.02340.0753-0.01230.0240.1512-0.01140.1235-18.74980.285616.8086
225.59552.30771.101712.7782-1.005610.14270.040.9859-0.5879-1.00420.26780.35240.8129-0.5577-0.30770.3396-0.0006-0.06920.4065-0.06130.29435.514650.205310.9326
238.13850.79635.8662.9647-0.30627.77970.1562-0.0246-0.36450.1094-0.05550.10140.2425-0.0161-0.10070.0906-0.00170.03420.1061-0.0090.096647.047954.566724.7849
244.73210.53020.53220.20870.00550.11370.0654-0.07830.25320.1217-0.04890.134-0.0521-0.0617-0.01660.1367-0.00070.03230.147-0.01290.167640.812561.327922.9318
252.03291.4816.83398.5279-3.576833.0706-0.1954-0.0330.2898-0.02970.41690.9217-0.6934-0.7214-0.22150.09130.01650.01580.19830.03150.648730.040469.192524.1933
266.4813-1.1042-1.0162.8349-0.73714.94120.0795-0.05560.45460.2012-0.00020.1682-0.1758-0.1927-0.07930.1081-0.0280.02080.0726-0.05970.144947.783969.763525.3857
2720.43074.27935.563910.4132-1.79622.4488-0.11470.58890.0089-0.0927-0.0049-0.5098-0.01310.12770.11960.27460.02690.02110.40420.06420.242237.78766.743414.0126
285.88911.40941.74680.69480.42910.6093-0.16650.29530.6118-0.08320.02250.3091-0.1405-0.02140.1440.2388-0.007-0.01180.2710.01360.252433.57267.339418.6478
294.4036-1.8235-0.84134.94191.85179.77870.17120.3820.0264-0.69860.0897-0.2510.2080.4993-0.26090.1671-0.00760.01510.2309-0.05560.159242.738139.167512.9476
302.0691-1.5275-0.35683.84521.73351.8120.0232-0.09280.01920.04510.02950.1208-0.0063-0.0289-0.05270.0623-0.01640.02060.1205-0.01740.108931.039543.950224.0462
3114.7605-0.6869-1.91621.4138-2.36664.6208-0.0597-0.6954-0.56510.03950.18270.1352-0.0398-0.222-0.1230.1927-0.0412-0.01150.2069-0.03220.195933.431726.18125.3951
324.6232-3.93654.01789.4939-0.96734.93380.0346-0.4073-0.11370.2919-0.03870.5433-0.0158-0.45160.0040.0852-0.02160.07580.16230.01020.217621.595341.904927.3639
339.3527-9.5938-6.308210.29264.463313.35360.21140.0943-0.5773-0.3648-0.12120.71350.1545-0.324-0.09020.14680.0401-0.09460.2239-0.03870.396318.299939.800618.6213
3435.6305-7.2722.87858.0411-1.78020.47960.06830.60470.7818-0.4583-0.04390.06030.0957-0.0486-0.02440.18030.0324-0.0590.29650.02990.177731.544831.201714.6942
357.0218-4.988-2.08415.09062.87942.78840.15540.3734-0.3872-0.0679-0.25650.4510.1499-0.20110.10110.0871-0.0513-0.00130.07470.00240.167729.285328.561218.9428
361.50081.3994.60635.555-0.992421.3789-0.1985-0.05410.0996-1.04280.0161-0.0495-0.2508-0.63560.18240.65150.2350.1730.50060.16320.538249.548453.58369.8672
373.84582.5819-0.87619.3644-6.54448.29350.0735-0.02160.06470.26720.16790.1368-0.1572-0.2893-0.24140.08370.02350.00130.133-0.0420.084248.725740.218723.1537
381.73541.6590.17645.42930.39010.03190.0439-0.2047-0.11760.0211-0.0206-0.36450.0022-0.0212-0.02330.1033-0.0105-0.01690.13330.00520.102657.976842.510822.6135
3911.7104-11.54953.183714.4752-3.485617.4419-0.1522-0.3336-0.09980.18170.0789-0.310.30470.79780.07340.2055-0.0218-0.02690.2486-0.0490.25468.93345.632125.9555
404.68992.395-0.18338.133.03977.0521-0.0329-0.3294-0.15760.29410.0605-0.40240.14050.26-0.02770.08880.0104-0.10580.10360.02790.143859.963330.305925.5102
410.15971.07570.137610.26461.5982.8178-0.01590.0827-0.1408-0.36180.0281-0.5565-0.11110.1362-0.01220.09760.01730.04120.2207-0.0690.298463.928646.507916.2101
422.7994.9762-2.266811.2752-7.78477.7794-0.08020.0948-0.5389-0.4161-0.3402-1.0110.270.77510.42040.23950.0320.12640.1407-0.05560.360166.716839.319419.2569
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 10
2X-RAY DIFFRACTION2A11 - 41
3X-RAY DIFFRACTION3A42 - 53
4X-RAY DIFFRACTION4A54 - 59
5X-RAY DIFFRACTION5A60 - 76
6X-RAY DIFFRACTION6A77 - 90
7X-RAY DIFFRACTION7A91 - 100
8X-RAY DIFFRACTION8B3 - 12
9X-RAY DIFFRACTION9B13 - 22
10X-RAY DIFFRACTION10B23 - 47
11X-RAY DIFFRACTION11B48 - 61
12X-RAY DIFFRACTION12B62 - 76
13X-RAY DIFFRACTION13B77 - 90
14X-RAY DIFFRACTION14B91 - 100
15X-RAY DIFFRACTION15C1 - 10
16X-RAY DIFFRACTION16C11 - 43
17X-RAY DIFFRACTION17C44 - 53
18X-RAY DIFFRACTION18C54 - 59
19X-RAY DIFFRACTION19C60 - 73
20X-RAY DIFFRACTION20C74 - 80
21X-RAY DIFFRACTION21C81 - 100
22X-RAY DIFFRACTION22D1 - 11
23X-RAY DIFFRACTION23D12 - 27
24X-RAY DIFFRACTION24D28 - 52
25X-RAY DIFFRACTION25D53 - 57
26X-RAY DIFFRACTION26D58 - 78
27X-RAY DIFFRACTION27D79 - 83
28X-RAY DIFFRACTION28D84 - 100
29X-RAY DIFFRACTION29E1 - 15
30X-RAY DIFFRACTION30E16 - 46
31X-RAY DIFFRACTION31E47 - 60
32X-RAY DIFFRACTION32E61 - 72
33X-RAY DIFFRACTION33E73 - 78
34X-RAY DIFFRACTION34E79 - 85
35X-RAY DIFFRACTION35E86 - 100
36X-RAY DIFFRACTION36F1 - 8
37X-RAY DIFFRACTION37F9 - 28
38X-RAY DIFFRACTION38F29 - 53
39X-RAY DIFFRACTION39F54 - 59
40X-RAY DIFFRACTION40F60 - 76
41X-RAY DIFFRACTION41F77 - 90
42X-RAY DIFFRACTION42F91 - 100

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