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- PDB-3l7y: The Crystal Structure of SMU.1108c from Streptococcus mutans UA159 -

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Basic information

Entry
Database: PDB / ID: 3l7y
TitleThe Crystal Structure of SMU.1108c from Streptococcus mutans UA159
ComponentsPutative uncharacterized protein smu.1108c
KeywordsHYDROLASE
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich ...Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.996 Å
AuthorsSu, X.-D. / Feng, M.J. / Liu, X.
CitationJournal: TO BE PUBLISHED
Title: The Crystal Structure of SMU.1108c from Streptococcus mutans UA159
Authors: Su, X.-D. / Feng, M.J. / Liu, X.
History
DepositionDec 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_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: Putative uncharacterized protein smu.1108c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1512
Polymers34,1271
Non-polymers241
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.094, 80.198, 47.937
Angle α, β, γ (deg.)90.00, 99.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-28-

ARG

21A-335-

HOH

31A-432-

HOH

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Components

#1: Protein Putative uncharacterized protein smu.1108c


Mass: 34126.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: smu.1108c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DU45
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M tris pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Sep 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.996→55.2 Å / Num. all: 19487 / Num. obs: 17580 / % possible obs: 90.21 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 16.29 Å2
Reflection shellResolution: 1.996→2.15 Å / % possible all: 55.9

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RLM

1rlm


Resolution: 1.996→55.177 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.809 / SU ML: 0.28 / σ(F): 0.04 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 1688 10 %
Rwork0.1843 15184 -
obs0.1905 16872 86.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.898 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 142.67 Å2 / Biso mean: 23.179 Å2 / Biso min: 5.63 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.996→55.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 1 162 2246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072115
X-RAY DIFFRACTIONf_angle_d1.3792847
X-RAY DIFFRACTIONf_dihedral_angle_d16.049755
X-RAY DIFFRACTIONf_chiral_restr0.07315
X-RAY DIFFRACTIONf_plane_restr0.007370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9965-2.05520.3252540.201514X-RAY DIFFRACTION36
2.0552-2.12160.3077840.2115779X-RAY DIFFRACTION54
2.1216-2.19740.26961320.19981189X-RAY DIFFRACTION80
2.1974-2.28540.271450.19221298X-RAY DIFFRACTION88
2.2854-2.38940.30571490.19541328X-RAY DIFFRACTION91
2.3894-2.51540.2461520.17751357X-RAY DIFFRACTION93
2.5154-2.6730.25041560.19521399X-RAY DIFFRACTION95
2.673-2.87930.25721620.18741424X-RAY DIFFRACTION98
2.8793-3.16910.25551610.18951447X-RAY DIFFRACTION99
3.1691-3.62760.23931640.18571480X-RAY DIFFRACTION99
3.6276-4.570.19011630.14561476X-RAY DIFFRACTION100
4.57-55.19850.20821660.17041493X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 18.9702 Å / Origin y: 28.727 Å / Origin z: 15.5221 Å
111213212223313233
T0.0933 Å2-0.0489 Å2-0.0125 Å2-0.2376 Å20.0085 Å2--0.007 Å2
L0.1392 °20.0888 °2-0.1239 °2-0.1759 °2-0.0902 °2--0.6474 °2
S-0.0504 Å °-0.0146 Å °0.0051 Å °-0.0249 Å °0.0171 Å °-0.007 Å °-0.0885 Å °0.2721 Å °0.0259 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 268
2X-RAY DIFFRACTION1allA1 - 448
3X-RAY DIFFRACTION1allA1 - 271

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