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- PDB-4cex: 1.59 A resolution Fluoride inhibited Sporosarcina pasteurii urease -

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Basic information

Entry
Database: PDB / ID: 4cex
Title1.59 A resolution Fluoride inhibited Sporosarcina pasteurii urease
Components(UREASE SUBUNIT ...) x 3
KeywordsHYDROLASE / NAF
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
FLUORIDE ION / NICKEL (II) ION / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesSPOROSARCINA PASTEURII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.589 Å
AuthorsBenini, S. / Cianci, M. / Ciurli, S.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2014
Title: Fluoride Inhibition of Sporosarcina Pasteurii Urease: Structure and Thermodynamics.
Authors: Benini, S. / Cianci, M. / Mazzei, L. / Ciurli, S.
#1: Journal: J.Biol.Inorg.Chem. / Year: 2013
Title: The Crystal Structure of Sporosarcina Pasteurii Urease in a Complex with Citrate Provides New Hints for Inhibitor Design.
Authors: Benini, S. / Kosikowska, P. / Cianci, M. / Mazzei, L. / Vara, A.G. / Berlicki, L. / Ciurli, S.
#2: Journal: J.Am.Chem.Soc. / Year: 2004
Title: Molecular Details of Urease Inhibition by Boric Acid: Insights Into the Catalytic Mechanism.
Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Mangani, S. / Ciurli, S.
#3: Journal: J.Biol.Inorg.Chem. / Year: 2001
Title: Structure-Based Rationalization of Urease Inhibition by Phosphate: Novel Insights Into the Enzyme Mechanism.
Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Ciurli, S. / Mangani, S.
#4: Journal: J.Biol.Inorg.Chem. / Year: 2000
Title: The Complex of Bacillus Pasteurii Urease with Acetohydroxamate Anion from X-Ray Data at 1.55 A Resolution.
Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Miletti, S. / Ciurli, S. / Mangani, S.
#5: Journal: Structure / Year: 1999
Title: A New Proposal for Urease Mechanism Based on the Crystal Structures of the Native and Inhibited Enzyme from Bacillus Pasteurii: Why Urea Hydrolysis Costs Two Nickels.
Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Miletti, S. / Ciurli, S. / Mangani, S.
#6: Journal: J.Biol.Inorg.Chem. / Year: 1998
Title: The Complex of Bacillus Pasteurii Urease with Beta-Mercaptoethanol from X-Ray Data at 1.65 A Resolution
Authors: Benini, S. / Ciurli, S. / Rypniewski, W.R. / Wilson, K.S. / Mangani, S.
#7: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and Preliminary High-Resolution X-Ray Diffraction Analysis of Native and Beta-Mercaptoethanol-Inhibited Urease from Bacillus Pasteurii.
Authors: Benini, S. / Ciurli, S. / Rypniewski, W.R. / Wilson, K.S. / Mangani, S.
History
DepositionNov 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Data collection / Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: 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.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.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)87,95421
Polymers86,8273
Non-polymers1,12618
Water14,880826
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)263,86163
Polymers260,4829
Non-polymers3,37954
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 area56640 Å2
ΔGint-252.9 kcal/mol
Surface area59290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.331, 131.331, 188.882
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-1580-

SO4

21C-1580-

SO4

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Components

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

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


Mass: 11204.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) SPOROSARCINA PASTEURII (bacteria) / Strain: DSM33 / References: UniProt: P41022, urease
#2: Protein UREASE SUBUNIT BETA / UREASE / 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) / Strain: DSM33 / References: UniProt: P41021, urease
#3: Protein UREASE SUBUNIT ALPHA / UREASE / UREA AMIDOHYDROLASE SUBUNIT ALPHA


Mass: 61646.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) SPOROSARCINA PASTEURII (bacteria) / Strain: DSM33 / References: UniProt: P41020, urease

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Non-polymers , 5 types, 844 molecules

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


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / 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-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 826 / 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: 2.73 Å3/Da / Density % sol: 55.01 % / Description: NONE
Crystal growpH: 6.5
Details: 1.8 M AMMONIUM SULPHATE, 50 MM SODIUM SULPHITE, 50 MM SODIUM CITRATE, 100 MM SODIUM FLUORIDE, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.968
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2012
RadiationMonochromator: SI (III) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.59→113.74 Å / Num. obs: 128776 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 14.4 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.7
Reflection shellResolution: 1.59→1.63 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AC7

4ac7


Resolution: 1.589→113.736 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.926 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.057 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1502 6458 5.02 %RANDOM
Rwork0.1297 ---
obs0.131 128593 99.808 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.824 Å2
Baniso -1Baniso -2Baniso -3
1-0.372 Å20.372 Å20 Å2
2--0.372 Å20 Å2
3----1.207 Å2
Refinement stepCycle: LAST / Resolution: 1.589→113.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6014 0 63 826 6903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196264
X-RAY DIFFRACTIONr_bond_other_d0.0010.026047
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9748476
X-RAY DIFFRACTIONr_angle_other_deg0.822313950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2875815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07624.797271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.944151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7421538
X-RAY DIFFRACTIONr_chiral_restr0.0920.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217109
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021320
X-RAY DIFFRACTIONr_nbd_refined0.2640.22252
X-RAY DIFFRACTIONr_nbd_other0.1870.2268
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23045
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2186
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_it1.1671.2856264
X-RAY DIFFRACTIONr_mcbond_other0.2471.3126047
X-RAY DIFFRACTIONr_mcangle_it1.8451.8998461
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3883.946729
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.58114.4085276
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: 1.589→1.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 519 -
Rwork0.17 8776 -
obs--99.094 %

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