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- PDB-3msr: The crystal structure of an amidohydrolase from Mycoplasma synoviae -

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Basic information

Entry
Database: PDB / ID: 3msr
TitleThe crystal structure of an amidohydrolase from Mycoplasma synoviae
Componentsamidohydrolases
KeywordsHYDROLASE / amidohydrolases / HAD / PSI / SGX / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


5-phospho-D-xylono-1,4-lactonase / 1,4-lactonase / 1,4-lactonase activity / catabolic process / zinc ion binding
Similarity search - Function
: / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phospho-furanose lactonase
Similarity search - Component
Biological speciesMycoplasma synoviae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.162 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of an amidohydrolase from Mycoplasma synoviae
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: amidohydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2853
Polymers41,0981
Non-polymers1872
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: amidohydrolases
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)247,71218
Polymers246,5906
Non-polymers1,12212
Water1086
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
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area19760 Å2
ΔGint-134 kcal/mol
Surface area69070 Å2
MethodPISA
3
A: amidohydrolases
hetero molecules

A: amidohydrolases
hetero molecules

A: amidohydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8569
Polymers123,2953
Non-polymers5616
Water543
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 area6970 Å2
ΔGint-44 kcal/mol
Surface area37450 Å2
MethodPISA
4
A: amidohydrolases
hetero molecules

A: amidohydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5716
Polymers82,1972
Non-polymers3744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area2710 Å2
ΔGint-30 kcal/mol
Surface area26900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.248, 111.248, 138.308
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein amidohydrolases


Mass: 41098.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma synoviae (bacteria) / Strain: 53 / Gene: HAD, MS53_0025 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3)+codon+RIL (p)-stratagene
References: UniProt: Q4A724
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Potassium sodium tartrate tetrahydate, 0.1 M Sodium citrate tribasic dihydrate pH5.6, 2.0 M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 27549 / % possible obs: 99.4 % / Redundancy: 29.7 % / Biso Wilson estimate: 15.44 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.1
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 29.5 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2673 / % possible all: 99

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.162→41.587 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1387 5.04 %RANDOM
Rwork0.1503 ---
obs0.1524 27521 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.61 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 15.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.0018 Å20 Å2-0 Å2
2--0.0018 Å20 Å2
3----0.0035 Å2
Refinement stepCycle: LAST / Resolution: 2.162→41.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 11 295 3087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192851
X-RAY DIFFRACTIONf_angle_d1.5913848
X-RAY DIFFRACTIONf_dihedral_angle_d19.6481064
X-RAY DIFFRACTIONf_chiral_restr0.112435
X-RAY DIFFRACTIONf_plane_restr0.008491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1616-2.23880.19171280.13442538X-RAY DIFFRACTION99
2.2388-2.32850.19391430.13852533X-RAY DIFFRACTION99
2.3285-2.43440.21771370.1412553X-RAY DIFFRACTION99
2.4344-2.56280.20881220.14562573X-RAY DIFFRACTION99
2.5628-2.72330.21021500.15232575X-RAY DIFFRACTION99
2.7233-2.93350.21011420.15812585X-RAY DIFFRACTION100
2.9335-3.22860.20611340.1632609X-RAY DIFFRACTION100
3.2286-3.69560.16151460.14912632X-RAY DIFFRACTION100
3.6956-4.6550.17691320.12912689X-RAY DIFFRACTION100
4.655-41.59420.18091530.16632847X-RAY DIFFRACTION100

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