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- PDB-5fse: 2.07 A resolution 1,4-Benzoquinone inhibited Sporosarcina pasteur... -

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Basic information

Entry
Database: PDB / ID: 5fse
Title2.07 A resolution 1,4-Benzoquinone inhibited Sporosarcina pasteurii urease
Components(UREASE SUBUNIT ...) x 3
KeywordsHYDROLASE / UREASE / SPOROSARCINA PASTEURII / NICKEL / METALLOENZYME / 1 / 4-BENZOQUINONE
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
benzene-1,4-diol / NICKEL (II) ION / HYDROXIDE ION / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesSPOROSARCINA PASTEURII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsMazzei, L. / Cianci, M. / Musiani, F. / Ciurli, S.
CitationJournal: Dalton Trans / Year: 2016
Title: Inactivation of Urease by 1,4-Benzoquinone: Chemistry at the Protein Surface.
Authors: Mazzei, L. / Cianci, M. / Musiani, F. / Ciurli, S.
History
DepositionJan 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UREASE SUBUNIT GAMMA
B: UREASE SUBUNIT BETA
C: UREASE SUBUNIT ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,52627
Polymers86,6863
Non-polymers1,84024
Water8,359464
1
A: UREASE SUBUNIT GAMMA
B: UREASE SUBUNIT BETA
C: UREASE SUBUNIT ALPHA
hetero molecules

A: UREASE SUBUNIT GAMMA
B: UREASE SUBUNIT BETA
C: UREASE SUBUNIT ALPHA
hetero molecules

A: UREASE SUBUNIT GAMMA
B: UREASE SUBUNIT BETA
C: UREASE SUBUNIT ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,57881
Polymers260,0589
Non-polymers5,52072
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area60510 Å2
ΔGint-557.7 kcal/mol
Surface area60090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.834, 131.834, 188.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11C-2046-

HOH

21C-2253-

HOH

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Components

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UREASE SUBUNIT ... , 3 types, 3 molecules ABC

#1: Protein UREASE SUBUNIT GAMMA / UREA AMIDOHYDROLASE SUBUNIT GAMMA


Mass: 11134.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) SPOROSARCINA PASTEURII (bacteria) / Variant: DSM 33 / References: UniProt: P41022, urease
#2: Protein UREASE SUBUNIT BETA / UREA AMIDOHYDROLASE SUBUNIT BETA


Mass: 13975.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) SPOROSARCINA PASTEURII (bacteria) / Variant: DSM 33 / References: UniProt: P41021, urease
#3: Protein UREASE SUBUNIT ALPHA / UREA AMIDOHYDROLASE SUBUNIT ALPHA


Mass: 61575.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) SPOROSARCINA PASTEURII (bacteria) / Variant: DSM 33 / References: UniProt: P41020, urease

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Non-polymers , 6 types, 488 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#8: Chemical ChemComp-HQE / benzene-1,4-diol


Mass: 110.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details2,5-DIHYDROXYBENZENE (DBX): DBX LIGAND HAS BEEN USED TO DESCRIBE AN HYDROQUINONE, THE LATTER BEING ...2,5-DIHYDROXYBENZENE (DBX): DBX LIGAND HAS BEEN USED TO DESCRIBE AN HYDROQUINONE, THE LATTER BEING THE ACTUAL LIGAND FOUND IN THE CRYSTAL STRUCTURE

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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: 2.76 Å3/Da / Density % sol: 55.5 % / Description: NONE
Crystal growpH: 6.3
Details: 1.8 M AMMONIUM SULFATE, 50 MM SODIUM CITRATE BUFFER PH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.954
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.07→188.58 Å / Num. obs: 58491 / % possible obs: 98.8 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9
Reflection shellResolution: 2.07→2.13 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.6 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AC7

4ac7


Resolution: 2.07→114.17 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.797 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19194 2944 5 %RANDOM
Rwork0.14482 ---
obs0.14717 55538 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.104 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.46 Å20 Å2
2--0.93 Å20 Å2
3----3.01 Å2
Refinement stepCycle: LAST / Resolution: 2.07→114.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6046 0 104 464 6614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196445
X-RAY DIFFRACTIONr_bond_other_d0.0020.026187
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.9778732
X-RAY DIFFRACTIONr_angle_other_deg0.868314291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4715836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48925.018281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.294151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5031537
X-RAY DIFFRACTIONr_chiral_restr0.1060.2977
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217363
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021364
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0582.7413267
X-RAY DIFFRACTIONr_mcbond_other2.0522.7413266
X-RAY DIFFRACTIONr_mcangle_it2.9364.1024112
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4063.2023178
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 204 -
Rwork0.267 3989 -
obs--97.26 %

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