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- PDB-4epb: Final Urease Structure for Radiation Damage Experiment at 100 K -

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Basic information

Entry
Database: PDB / ID: 4epb
TitleFinal Urease Structure for Radiation Damage Experiment at 100 K
Components
  • Urease subunit alpha
  • Urease subunit beta
  • Urease subunit gamma
KeywordsHYDROLASE / alpha-beta barrel / nickel metalloenzyme / radiation damage
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like subunit / Urease, gamma subunit / : / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. ...Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like subunit / Urease, gamma subunit / : / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / 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
NICKEL (II) ION / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesEnterobacter aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWarkentin, M. / Badeau, R. / Hopkins, J.B. / Thorne, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Spatial distribution of radiation damage to crystalline proteins at 25-300 K.
Authors: Warkentin, M. / Badeau, R. / Hopkins, J.B. / Thorne, R.E.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

Downloads & links

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Assembly

Deposited unit
C: Urease subunit alpha
B: Urease subunit beta
A: Urease subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6225
Polymers82,5053
Non-polymers1172
Water11,746652
1
C: Urease subunit alpha
B: Urease subunit beta
A: Urease subunit gamma
hetero molecules

C: Urease subunit alpha
B: Urease subunit beta
A: Urease subunit gamma
hetero molecules

C: Urease subunit alpha
B: Urease subunit beta
A: Urease subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,86715
Polymers247,5149
Non-polymers3526
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area47600 Å2
ΔGint-318 kcal/mol
Surface area56960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.212, 169.212, 169.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Urease subunit alpha / Urea amidohydrolase subunit alpha


Mass: 60278.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter aerogenes (bacteria) / Gene: ureC / Production host: Escherichia coli (E. coli) / References: UniProt: P18314, urease
#2: Protein Urease subunit beta / Urea amidohydrolase subunit beta


Mass: 11125.690 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter aerogenes (bacteria) / Gene: ureB / Production host: Escherichia coli (E. coli) / References: UniProt: P18315, urease
#3: Protein Urease subunit gamma / Urea amidohydrolase subunit gamma


Mass: 11100.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter aerogenes (bacteria) / Gene: ureA / Production host: Escherichia coli (E. coli) / References: UniProt: P18316, urease
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: lithium sulfate, hepes, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 24, 2011
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 80390 / % possible obs: 99.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.048 / Χ2: 1.466 / Net I/σ(I): 17.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.784.40.63939980.8941100
1.78-1.814.40.51240180.9241100
1.81-1.854.40.43240240.9691100
1.85-1.894.50.34340150.9591100
1.89-1.934.40.27640161.041100
1.93-1.974.50.22239711.0591100
1.97-2.024.50.18240301.1521100
2.02-2.074.50.14840091.2161100
2.07-2.144.50.12140401.2611100
2.14-2.24.50.10840201.3521100
2.2-2.284.50.08840311.3951100
2.28-2.384.50.07840071.491100
2.38-2.484.50.06940821.6151100
2.48-2.614.50.06140141.6581100
2.61-2.784.50.05340471.809199.9
2.78-2.994.50.04640371.899199.8
2.99-3.294.50.03840432.052199.5
3.29-3.774.40.03140202.104198.9
3.77-4.754.40.02740032.035197.9
4.75-504.40.03239652.485194.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.8.0phasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→30.89 Å / Cor.coef. Fo:Fc: 0.9674 / Cor.coef. Fo:Fc free: 0.9552 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 4023 5.02 %RANDOM
Rwork0.1713 ---
obs0.1726 80111 --
Displacement parametersBiso max: 103.03 Å2 / Biso mean: 29.0943 Å2 / Biso min: 14.28 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.185 Å
Refinement stepCycle: LAST / Resolution: 1.75→30.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 2 652 6444
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2001SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes144HARMONIC2
X-RAY DIFFRACTIONt_gen_planes876HARMONIC5
X-RAY DIFFRACTIONt_it5906HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion1HARMONIC0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion796SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7306SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5906HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8032HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.75
X-RAY DIFFRACTIONt_other_torsion16.37
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2934 296 5.04 %
Rwork0.2343 5579 -
all0.2372 5875 -

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