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- PDB-3ovg: The crystal structure of an amidohydrolase from Mycoplasma synovi... -

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Basic information

Entry
Database: PDB / ID: 3ovg
TitleThe crystal structure of an amidohydrolase from Mycoplasma synoviae with Zn ion bound
Componentsamidohydrolase
KeywordsHYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / amidohydrolases / HAD / PSI / SGX / Zn
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 / MOLECULAR REPLACEMENT / Resolution: 2.059 Å
AuthorsZhang, Z. / Kumaran, D. / 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 with Zn ion bound
Authors: Zhang, Z. / Kumaran, D. / Burley, S.K. / Swaminathan, S.
History
DepositionSep 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: amidohydrolase
B: amidohydrolase
C: amidohydrolase
D: amidohydrolase
E: amidohydrolase
F: amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,20224
Polymers246,8486
Non-polymers1,35518
Water21,3481185
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19240 Å2
ΔGint-610 kcal/mol
Surface area67840 Å2
MethodPISA
2
A: amidohydrolase
B: amidohydrolase
E: amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,10112
Polymers123,4243
Non-polymers6779
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-283 kcal/mol
Surface area36990 Å2
MethodPISA
3
A: amidohydrolase
F: amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7348
Polymers82,2832
Non-polymers4526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-188 kcal/mol
Surface area26180 Å2
MethodPISA
4
B: amidohydrolase
C: amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7348
Polymers82,2832
Non-polymers4526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-188 kcal/mol
Surface area26220 Å2
MethodPISA
5
C: amidohydrolase
D: amidohydrolase
F: amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,10112
Polymers123,4243
Non-polymers6779
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-281 kcal/mol
Surface area36730 Å2
MethodPISA
6
D: amidohydrolase
E: amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7348
Polymers82,2832
Non-polymers4526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-190 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.256, 89.186, 96.059
Angle α, β, γ (deg.)98.95, 92.89, 119.86
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
amidohydrolase


Mass: 41141.273 Da / Num. of mol.: 6
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1185 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4 M Sodium malonate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 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: 2.059→50 Å / Num. obs: 152064 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 4.9
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 4.9 / Num. unique all: 14991 / % possible all: 96.3

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MSR

3msr


Resolution: 2.059→43.747 Å / SU ML: 0.26 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 7629 5.02 %RANDOM
Rwork0.1724 ---
obs0.1743 151931 97.75 %-
all-152064 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.748 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 19.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.2092 Å20.8013 Å2-0.2209 Å2
2---0.2518 Å20.6802 Å2
3---0.461 Å2
Refinement stepCycle: LAST / Resolution: 2.059→43.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16602 0 42 1185 17829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01416989
X-RAY DIFFRACTIONf_angle_d1.41722940
X-RAY DIFFRACTIONf_dihedral_angle_d18.5456348
X-RAY DIFFRACTIONf_chiral_restr0.0962586
X-RAY DIFFRACTIONf_plane_restr0.0082933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.059-2.08240.30041930.21254288X-RAY DIFFRACTION86
2.0824-2.10690.24152670.1874697X-RAY DIFFRACTION97
2.1069-2.13260.23182490.17744872X-RAY DIFFRACTION97
2.1326-2.15960.23082280.17884707X-RAY DIFFRACTION97
2.1596-2.1880.24652630.17384820X-RAY DIFFRACTION97
2.188-2.2180.22712430.16844781X-RAY DIFFRACTION97
2.218-2.24960.22582610.17324794X-RAY DIFFRACTION97
2.2496-2.28320.22792740.17414809X-RAY DIFFRACTION97
2.2832-2.31890.25532570.16764697X-RAY DIFFRACTION98
2.3189-2.35690.21722500.16714846X-RAY DIFFRACTION97
2.3569-2.39750.20922680.16454816X-RAY DIFFRACTION98
2.3975-2.44110.21642430.16324783X-RAY DIFFRACTION98
2.4411-2.48810.20512530.16794889X-RAY DIFFRACTION98
2.4881-2.53890.21422650.16764780X-RAY DIFFRACTION98
2.5389-2.59410.19572380.16234820X-RAY DIFFRACTION98
2.5941-2.65440.23582490.17054837X-RAY DIFFRACTION98
2.6544-2.72080.21882370.1724895X-RAY DIFFRACTION98
2.7208-2.79430.21692530.17184818X-RAY DIFFRACTION98
2.7943-2.87650.21892470.18194876X-RAY DIFFRACTION99
2.8765-2.96940.23252550.18114803X-RAY DIFFRACTION98
2.9694-3.07550.21852840.18834855X-RAY DIFFRACTION99
3.0755-3.19860.21982490.18834879X-RAY DIFFRACTION99
3.1986-3.34410.21622450.18324818X-RAY DIFFRACTION99
3.3441-3.52030.19082410.16844885X-RAY DIFFRACTION99
3.5203-3.74080.18812610.16874894X-RAY DIFFRACTION99
3.7408-4.02940.18262900.15854829X-RAY DIFFRACTION99
4.0294-4.43460.19652700.15434865X-RAY DIFFRACTION99
4.4346-5.07540.17152660.14624856X-RAY DIFFRACTION99
5.0754-6.39130.18622730.17284919X-RAY DIFFRACTION99
6.3913-43.7570.18712570.17894874X-RAY DIFFRACTION100

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