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- PDB-4ac7: The crystal structure of Sporosarcina pasteurii urease in complex... -

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Basic information

Entry
Database: PDB / ID: 4ac7
TitleThe crystal structure of Sporosarcina pasteurii urease in complex with citrate
Components(UREASE SUBUNIT ...) x 3
KeywordsHYDROLASE / BACILLUS PASTEURII
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, beta subunit ...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
CITRATE ANION / 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 / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsBenini, S. / Kosikowska, P. / Cianci, M. / Gonzalez Vara, A. / Berlicki, L. / Ciurli, S.
Citation
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.
#1: 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.
#2: 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.
#3: 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.
#4: 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.
#5: 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.
#6: 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
DepositionDec 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Dec 3, 2014Group: Data collection
Revision 1.3Mar 14, 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 / pdbx_struct_special_symmetry / 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.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)88,15621
Polymers86,8273
Non-polymers1,32818
Water12,088671
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)264,46763
Polymers260,4829
Non-polymers3,98554
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 area57170 Å2
ΔGint-291 kcal/mol
Surface area59650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.555, 131.555, 189.521
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-1581-

SO4

21C-2071-

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: 11204.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPOROSARCINA PASTEURII (bacteria) / Strain: DSM33 / 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 / Source: (natural) SPOROSARCINA PASTEURII (bacteria) / Strain: DSM33 / References: UniProt: P41021, urease
#3: Protein UREASE SUBUNIT ALPHA / / UREA AMIDOHYDROLASE SUBUNIT ALPHA


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

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Non-polymers , 6 types, 689 molecules

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


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


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


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


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#8: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 671 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsETHYLENE GLYCOL (EDO): PRESENT AS CRYOPROTECTANT CITRATE ANION (FLC): PRESENT AS A CRYSTALLISATION ...ETHYLENE GLYCOL (EDO): PRESENT AS CRYOPROTECTANT CITRATE ANION (FLC): PRESENT AS A CRYSTALLISATION BUFFER SULFATE ION (SO4): CRYSTALS GREW FROM 1.8 M AMMONIUM SULPHATE N-CARBOXYMETHIONINE (CXM): POST-TRANSLATIONAL MODIFICATION NICKEL (II) ION (NI): REQUIRED FOR CATALYSIS LYSINE NZ-CARBOXYLIC ACID (KCX): POST-TRANSLATIONAL MODIFICATION
Sequence detailsTHE AUTHOR STATES THAT THE RESIDUES LISTED IN SEQADV ARE WHAT IS SEEN IN THE DENSITY, AND IT IS NOT ...THE AUTHOR STATES THAT THE RESIDUES LISTED IN SEQADV ARE WHAT IS SEEN IN THE DENSITY, AND IT IS NOT CLEAR WHERE THE DISCREPANCIES ARISE FROM.

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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: 55.46 %
Crystal growpH: 6.3
Details: 1.8 M AMMONIUM SULPHATE, 100 MM CITRATE PH 6.3, 50 MM NA2SO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.1267
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 30, 2011
RadiationMonochromator: SI(III) CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1267 Å / Relative weight: 1
ReflectionResolution: 1.5→113.93 Å / Num. obs: 153738 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 15.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 22.6
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1S3T DEPLETED OF WATERS SULPHATES AND BORATE WAS USED AS A MODEL FOR RIGID BODY REFINEMENT FOLLOWED BY REFINEMENT AND MODEL BUILDING

1s3t


Resolution: 1.5→113.93 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.71 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14605 7712 5 %RANDOM
Rwork0.11703 ---
obs0.11847 145792 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.109 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.5→113.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6014 0 76 671 6761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196256
X-RAY DIFFRACTIONr_bond_other_d0.0010.024219
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9768468
X-RAY DIFFRACTIONr_angle_other_deg0.947310348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2595810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84724.778270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3221538
X-RAY DIFFRACTIONr_chiral_restr0.0870.2959
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021170
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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_restr2.383310474
X-RAY DIFFRACTIONr_sphericity_free24.6415172
X-RAY DIFFRACTIONr_sphericity_bonded7.086510876
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 541 -
Rwork0.17 9983 -
obs--99.93 %

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