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- PDB-6rp1: 1.49 A RESOLUTION OF SPOROSARCINA PASTEURII UREASE INHIBITED IN T... -

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Basic information

Entry
Database: PDB / ID: 6rp1
Title1.49 A RESOLUTION OF SPOROSARCINA PASTEURII UREASE INHIBITED IN THE PRESENCE OF NBPTO AT pH 6.5
Components(Urease subunit ...) x 3
KeywordsHYDROLASE / UREA / NICKEL / NBPTO
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, gamma subunit / : / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit ...Urease, subunit B / Urease, beta 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 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase / Ribbon / Mainly Beta
Similarity search - Domain/homology
DIAMIDOPHOSPHATE / NICKEL (II) ION / Urease subunit gamma / Urease subunit alpha / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsMazzei, L. / Cianci, M. / Benini, S. / Ciurli, S.
CitationJournal: Chemistry / Year: 2019
Title: The Impact of pH on Catalytically Critical Protein Conformational Changes: The Case of the Urease, a Nickel Enzyme.
Authors: Mazzei, L. / Cianci, M. / Benini, S. / Ciurli, S.
History
DepositionMay 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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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)87,96027
Polymers86,2403
Non-polymers1,72124
Water12,773709
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)263,88181
Polymers258,7199
Non-polymers5,16272
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area60930 Å2
ΔGint-386 kcal/mol
Surface area58930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.813, 131.813, 189.028
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-620-

SO4

21C-1075-

HOH

31C-1083-

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 / Source: (natural) Sporosarcina pasteurii (bacteria) / Variant: DSM33
References: UniProt: A0A0H3YGY5, UniProt: P41022*PLUS, urease
#2: Protein Urease subunit beta / Urea amidohydrolase subunit beta


Mass: 13529.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Variant: DSM33 / 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 / Source: (natural) Sporosarcina pasteurii (bacteria) / Variant: DSM33
References: UniProt: A0A0H3YL32, UniProt: P41020*PLUS, urease

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Non-polymers , 5 types, 733 molecules

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


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / 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-2PA / DIAMIDOPHOSPHATE


Mass: 96.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5N2O2P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.75 Å3/Da / Density % sol: 55.51 % / Description: Rice-shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein dissolved in 50 mM HEPES, pH 7.5, 2 mM EDTA, 4 mM NBPTO. Precipitant solution consisting of 100 mM citrate buffer, 1.7-1.9 M ammonium sulfate, 4 mM NBPTO, at pH 6.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2018
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.49→114.15 Å / Num. obs: 156618 / % possible obs: 99.8 % / Redundancy: 13.2 % / Biso Wilson estimate: 13.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.036 / Rrim(I) all: 0.133 / Net I/σ(I): 15.3
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.933 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7624 / CC1/2: 0.575 / Rpim(I) all: 0.607 / Rrim(I) all: 2.115 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OL4

5ol4


Resolution: 1.49→114.15 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.16 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.051 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15302 7859 5 %RANDOM
Rwork0.13619 ---
obs0.13702 148730 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.406 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å2-0 Å2
2--0.54 Å2-0 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 1.49→114.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6046 0 97 709 6852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196681
X-RAY DIFFRACTIONr_bond_other_d0.0010.026427
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9759044
X-RAY DIFFRACTIONr_angle_other_deg0.8314843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0475863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39225294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.749151159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8891539
X-RAY DIFFRACTIONr_chiral_restr0.0880.21009
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217658
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021418
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_it0.9911.6993395
X-RAY DIFFRACTIONr_mcbond_other0.9891.6993394
X-RAY DIFFRACTIONr_mcangle_it1.5322.5454277
X-RAY DIFFRACTIONr_mcangle_other1.5322.5454278
X-RAY DIFFRACTIONr_scbond_it1.87823286
X-RAY DIFFRACTIONr_scbond_other1.8781.9943283
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9412.884762
X-RAY DIFFRACTIONr_long_range_B_refined5.30714.77615
X-RAY DIFFRACTIONr_long_range_B_other5.30614.7077616
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 583 -
Rwork0.258 10804 -
obs--99.32 %

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