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- PDB-4epd: Initial Urease Structure for Radiation Damage Experiment at 300 K -

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Basic information

Entry
Database: PDB / ID: 4epd
TitleInitial Urease Structure for Radiation Damage Experiment at 300 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: 1.7 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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Water9,602533
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 operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area47710 Å2
ΔGint-317 kcal/mol
Surface area57550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.765, 170.765, 170.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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.: 533 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
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: 300 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: 1.7→50 Å / Num. obs: 90349 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.07 / Χ2: 1.546 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.734.70.644260.6921100
1.73-1.765.10.52745560.7231100
1.76-1.795.20.42844630.7521100
1.79-1.835.30.35944730.8211100
1.83-1.875.30.30345380.8771100
1.87-1.915.30.24144560.9271100
1.91-1.965.30.245190.9721100
1.96-2.025.30.16844951.0791100
2.02-2.075.30.13845051.1441100
2.07-2.145.30.11844751.2241100
2.14-2.225.30.145241.2541100
2.22-2.315.30.08645281.3251100
2.31-2.415.30.07644991.391100
2.41-2.545.30.06945101.5051100
2.54-2.75.30.06245431.6351100
2.7-2.915.30.05745191.8811100
2.91-3.25.30.05145442.1521100
3.2-3.665.20.0545502.7761100
3.66-4.615.10.04945763.428199.9
4.61-504.70.05646504.511198.7

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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: 1.7→19.63 Å / Cor.coef. Fo:Fc: 0.9726 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1641 4527 5.01 %RANDOM
Rwork0.1443 ---
obs0.1453 90290 --
Displacement parametersBiso max: 152.88 Å2 / Biso mean: 27.5419 Å2 / Biso min: 11.78 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.142 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 2 533 6325
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2073SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes907HARMONIC5
X-RAY DIFFRACTIONt_it6116HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion1HARMONIC0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion823SEMIHARMONIC5
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_contact7264SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6116HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8320HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.96
X-RAY DIFFRACTIONt_other_torsion16.5
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1987 333 5.04 %
Rwork0.2069 6269 -
all0.2065 6602 -

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