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- PDB-3nur: Crystal structure of a putative amidohydrolase from Staphylococcu... -

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Basic information

Entry
Database: PDB / ID: 3nur
TitleCrystal structure of a putative amidohydrolase from Staphylococcus aureus
ComponentsAmidohydrolase
KeywordsHYDROLASE / TIM barrel
Function / homology
Function and homology information


secondary metabolic process / photosystem I reaction center / carboxy-lyase activity / photosynthesis / chloroplast / hydrolase activity / metal ion binding / cytosol
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Amidohydrolase-related domain-containing protein / Photosystem I p700 chlorophyll A apoprotein A2
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsQiu, W. / Lam, R. / Romanov, V. / Lam, K. / Soloveychik, M. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: To be Published
Title: Crystal structure of a putative amidohydrolase from Staphylococcus aureus
Authors: Qiu, W. / Lam, R. / Romanov, V. / Lam, K. / Soloveychik, M. / Pai, E.F. / Chirgadze, N.Y.
History
DepositionJul 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: 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_ref_seq_dif / 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_ref_seq_dif.details / _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: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0972
Polymers41,0571
Non-polymers401
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Amidohydrolase
hetero molecules

A: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1934
Polymers82,1132
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5270 Å2
ΔGint-61 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.289, 99.160, 92.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Amidohydrolase


Mass: 41056.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SAOG_01574, SAV2580 / Production host: Escherichia coli (E. coli)
References: UniProt: C8N232, UniProt: A0A0H3K164*PLUS, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 35% PEG400, 0.2M Calcium Acetate, 0.1M Sodium Cacodylate, 0.2M Lithium Citrate, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.75→92.13 Å / Num. all: 38796 / Num. obs: 38713 / % possible obs: 99.8 % / Redundancy: 14.11 % / Biso Wilson estimate: 16.68 Å2 / Rmerge(I) obs: 0.1259 / Rsym value: 0.046 / Net I/σ(I): 18.02
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 13.98 % / Rmerge(I) obs: 0.5414 / Mean I/σ(I) obs: 4.22 / Num. unique all: 5900 / Rsym value: 0.2569 / % possible all: 98.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→63.78 Å / Cor.coef. Fo:Fc: 0.9428 / Cor.coef. Fo:Fc free: 0.9292 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 1931 5 %RANDOM
Rwork0.1692 ---
obs0.1705 38644 --
Displacement parametersBiso mean: 18.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.2954 Å20 Å20 Å2
2--1.5279 Å20 Å2
3----2.8232 Å2
Refine analyzeLuzzati coordinate error obs: 0.173 Å
Refinement stepCycle: LAST / Resolution: 1.75→63.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 1 242 2706
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0125472
X-RAY DIFFRACTIONt_angle_deg1.0234582
X-RAY DIFFRACTIONt_dihedral_angle_d8742
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes742
X-RAY DIFFRACTIONt_gen_planes3695
X-RAY DIFFRACTIONt_it254720
X-RAY DIFFRACTIONt_nbd45
X-RAY DIFFRACTIONt_omega_torsion3.79
X-RAY DIFFRACTIONt_other_torsion17.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3265
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_contact31594
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.1969 135 4.67 %
Rwork0.1767 2755 -
all0.1776 2890 -

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