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- PDB-3qgk: 3.0 A Model of Iron Containing Urease UreA2B2 from Helicobacter m... -

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Basic information

Entry
Database: PDB / ID: 3qgk
Title3.0 A Model of Iron Containing Urease UreA2B2 from Helicobacter mustelae (refined w/ no ordered solvent)
Components
  • Fusion of urease beta and gamma subunits
  • Urease subunit beta 2
KeywordsHYDROLASE / iron metalloenzyme / alpha-beta barrel / urease
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / identical protein binding / cytoplasm
Similarity search - Function
Urease, gamma-beta subunit / Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like subunit / : / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily ...Urease, gamma-beta subunit / Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like subunit / : / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit / Urease domain profile. / Urease alpha-subunit, N-terminal domain / Urease alpha-subunit, N-terminal domain / Urease, gamma/gamma-beta subunit / Urease, gamma subunit superfamily / : / Urease, gamma subunit / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Ribbon / Roll / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Urease subunit beta / urease
Similarity search - Component
Biological speciesHelicobacter mustelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsTronrud, D.E. / Robbins, A. / Karplus, P.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Iron-containing urease in a pathogenic bacterium.
Authors: Carter, E.L. / Tronrud, D.E. / Taber, S.R. / Karplus, P.A. / Hausinger, R.P.
History
DepositionJan 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion of urease beta and gamma subunits
C: Urease subunit beta 2
D: Fusion of urease beta and gamma subunits
F: Urease subunit beta 2
G: Fusion of urease beta and gamma subunits
I: Urease subunit beta 2
J: Fusion of urease beta and gamma subunits
L: Urease subunit beta 2
M: Fusion of urease beta and gamma subunits
O: Urease subunit beta 2
P: Fusion of urease beta and gamma subunits
R: Urease subunit beta 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)523,52224
Polymers522,85212
Non-polymers67012
Water00
1
A: Fusion of urease beta and gamma subunits
C: Urease subunit beta 2
D: Fusion of urease beta and gamma subunits
F: Urease subunit beta 2
G: Fusion of urease beta and gamma subunits
I: Urease subunit beta 2
J: Fusion of urease beta and gamma subunits
L: Urease subunit beta 2
M: Fusion of urease beta and gamma subunits
O: Urease subunit beta 2
P: Fusion of urease beta and gamma subunits
R: Urease subunit beta 2
hetero molecules

A: Fusion of urease beta and gamma subunits
C: Urease subunit beta 2
D: Fusion of urease beta and gamma subunits
F: Urease subunit beta 2
G: Fusion of urease beta and gamma subunits
I: Urease subunit beta 2
J: Fusion of urease beta and gamma subunits
L: Urease subunit beta 2
M: Fusion of urease beta and gamma subunits
O: Urease subunit beta 2
P: Fusion of urease beta and gamma subunits
R: Urease subunit beta 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,047,04348
Polymers1,045,70324
Non-polymers1,34024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)166.980, 223.940, 395.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Fusion of urease beta and gamma subunits / UreA2


Mass: 25142.035 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter mustelae (bacteria) / Strain: ATCC 43772 / LMG 18044 / NCTC 12198 / 12198 / Gene: HMU13020, ureA2 / Plasmid: pEC015 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold / References: UniProt: D3UJ81
#2: Protein
Urease subunit beta 2 / UreB2 / Urea amidohydrolase subunit beta 2


Mass: 61999.883 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter mustelae (bacteria) / Strain: ATCC 43772 / LMG 18044 / NCTC 12198 / 12198 / Gene: HMU13010, ureB2 / Plasmid: pEC015 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold / References: UniProt: D3UJ80, urease
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe

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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: 3.54 Å3/Da / Density % sol: 65.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 6.7 mg/ml protein, 6.7 mM Tris, 20% MPD, 0.07 M sodium acetate, 0.013 M calcium chloride, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2010
RadiationMonochromator: ASYMMETRIC CUT SINGLE CRYSTAL SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.998→67.292 Å / Num. all: 145678 / Num. obs: 145678 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 59.84 Å2 / Rmerge(I) obs: 0.201 / Rsym value: 0.201 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.165.10.8090.9102307201400.80994.3
3.16-3.355.60.5461.4109887196590.54697.2
3.35-3.596.50.3692121909188740.36999.1
3.59-3.877.70.2682.8136954177400.26899.7
3.87-4.249.30.213.5151734163960.21100
4.24-4.7410.60.174.2157872148650.17100
4.74-5.4811.30.1734.1147901131350.173100
5.48-6.7112.40.1674.3139048111920.167100
6.71-9.4915.80.0878.213800987250.087100
9.49-67.29216.20.04812.78029649520.04899.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å67.29 Å
Translation3 Å67.29 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.18data scaling
PHASER2.2.4phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
BOSbeamline control softwaredata collection
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EJX

1ejx


Resolution: 3→67.29 Å / Cor.coef. Fo:Fc: 0.9244 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 7283 5.01 %RANDOM
Rwork0.1771 ---
all0.1781 145355 --
obs0.1781 145355 --
Displacement parametersBiso max: 140.26 Å2 / Biso mean: 31.4444 Å2 / Biso min: 7 Å2
Baniso -1Baniso -2Baniso -3
1-0.6436 Å20 Å20 Å2
2---2.1771 Å20 Å2
3---1.5334 Å2
Refine analyzeLuzzati coordinate error obs: 0.339 Å
Refinement stepCycle: LAST / Resolution: 3→67.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36408 0 12 0 36420
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d12954SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes930HARMONIC20.0072
X-RAY DIFFRACTIONt_gen_planes5406HARMONIC50.0141
X-RAY DIFFRACTIONt_it37140HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion6HARMONIC01.246
X-RAY DIFFRACTIONt_chiral_improper_torsion4932SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact42290SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d37140HARMONIC20.0088
X-RAY DIFFRACTIONt_angle_deg50160HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion20.33
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2602 477 4.78 %
Rwork0.2417 9508 -
all0.2426 9985 -
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6628-0.07830.0340.34980.03590.39910.00650.1022-0.0072-0.0901-0.0015-0.0507-0.0050.0321-0.005-0.0386-0.01390.024-0.11140.0208-0.030515.2475-94.310282.3624
20.557-0.0709-0.0620.48410.040.2954-0.0068-0.02990.05740.06160.0062-0.0421-0.04240.03280.0006-0.065-0.0378-0.0095-0.08060.0257-0.004125.9124-69.9023119.611
30.3384-0.05510.10380.45160.01440.4357-0.0098-0.00990.0659-0.0287-0.0010.062-0.0116-0.03870.0108-0.08570.00290.0067-0.0970.05750.0266-17.0946-70.6866104.394
40.4776-0.0891-0.09420.6280.17550.4598-0.0033-0.0459-0.0081-0.010.0233-0.0988-0.01740.0921-0.02-0.0875-0.0144-0.0069-0.02040.0063-0.011849.3619-107.636133.655
50.456-0.009-0.10080.3359-0.05490.5451-0.0049-0.128-0.0910.05350.0164-0.05330.0497-0.0045-0.0115-0.03360.0243-0.0337-0.0295-0.0059-0.003629.326-145.885148.734
60.3840.1079-0.07090.4969-0.07290.45580.0022-0.1210.07670.09250.0154-0.0023-0.02970.0391-0.0176-0.00850.0415-0.01870.1034-0.0375-0.098522.675-106.328170.67
70.46920.0669-0.19670.9430.39621.29260.00320.08630.0986-0.1122-0.0289-0.0359-0.0155-0.06470.0256-0.0074-0.01230.0058-0.09620.122-0.01620.9554-62.925777.0586
81.8078-0.5850.20680.57770.79480.9232-0.01130.1090.0557-0.18470.0370.1126-0.0623-0.1373-0.0257-0.09590.0332-0.0571-0.030.0754-0.0317-34.093-94.082672.509
91.365-0.20920.94880.696-0.26421.19630.00730.0286-0.0132-0.02570.0069-0.1176-0.01860.0243-0.0143-0.0825-0.0770.0382-0.10130.07040.047728.1988-63.504585.3361
101.63790.0870.31661.37930.78811.1112-0.02160.1758-0.0206-0.0069-0.003-0.05020.04680.18380.0246-0.106-0.02270.0952-0.0661-0.0180.021456.382-100.37893.452
111.8673-0.8571-0.31680.49390.25850.8414-0.00930.00320.0761-0.00960.01040.0038-0.0169-0.0097-0.0011-0.0581-0.0435-0.0007-0.1930.07660.08999.1914-48.1743100.181
122.3630.2210.581900.06772.65710.0246-0.1880.16620.05170.0018-0.0506-0.07540.0339-0.02640.0150.005-0.0225-0.1171-0.07340.0293-0.2387-48.5767146.341
130.00110.0357-0.13610.8801-0.53530.834-0.0225-0.07570.01520.06840.0346-0.0257-0.0210.0874-0.0121-0.0974-0.0187-0.07150.1766-0.05340.026756.1241-108.504167.89
141.1021-0.0394-0.2451.8416-0.11160.6754-0.0103-0.22160.07010.08650.00760.0152-0.07870.04410.0028-0.0259-0.0556-0.01950.0228-0.1105-0.036635.71-66.8276159.754
150.13320.36510.06751.78230.31460.8340.0148-0.0251-0.0288-0.0320.0285-0.1356-0.0267-0.0449-0.0433-0.08220.0815-0.07920.0679-0.00110.091761.2687-132.438153.017
161.42350.828-0.63492.0205-0.31351.8647-0.00430.1558-0.0631-0.03360.0363-0.1290.02280.0723-0.032-0.14880.04360.0658-0.1153-0.06080.010656.5859-140.336106.805
170.9262-0.3384-0.96021.41330.43431.18440.0014-0.19440.04790.07310.0174-0.12130.0508-0.0019-0.0189-0.04670.06-0.09170.19420.012-0.11344.2853-133.248176.055
180.09450.5035-0.58962.42960.06150.06180.0185-0.0781-0.19940.16630.02980.05470.05790.0004-0.04830.1046-0.00340.0080.04980.0708-0.12330.6857-150.546180.494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ C|1 - C|568 }C1 - 568
2X-RAY DIFFRACTION2{ F|1 - F|568 }F1 - 568
3X-RAY DIFFRACTION3{ I|1 - I|568 }I1 - 568
4X-RAY DIFFRACTION4{ L|1 - L|568 }L1 - 568
5X-RAY DIFFRACTION5{ O|1 - O|568 }O1 - 568
6X-RAY DIFFRACTION6{ R|1 - R|568 }R1 - 568
7X-RAY DIFFRACTION7{ A|1 - A|108 }A1 - 108
8X-RAY DIFFRACTION8{ A|118 - A|225 }A118 - 225
9X-RAY DIFFRACTION9{ D|1 - D|108 }D1 - 108
10X-RAY DIFFRACTION10{ D|118 - D|225 }D118 - 225
11X-RAY DIFFRACTION11{ G|1 - G|108 }G1 - 108
12X-RAY DIFFRACTION12{ G|118 - G|225 }G118 - 225
13X-RAY DIFFRACTION13{ J|1 - J|108 }J1 - 108
14X-RAY DIFFRACTION14{ J|118 - J|225 }J118 - 225
15X-RAY DIFFRACTION15{ M|1 - M|108 }M1 - 108
16X-RAY DIFFRACTION16{ M|118 - M|225 }M118 - 225
17X-RAY DIFFRACTION17{ P|1 - P|108 }P1 - 108
18X-RAY DIFFRACTION18{ P|118 - P|225 }P118 - 225

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