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- PDB-3l7x: The Crystal Structure of SMU.412c from Streptococcus mutans UA159 -

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Basic information

Entry
Database: PDB / ID: 3l7x
TitleThe Crystal Structure of SMU.412c from Streptococcus mutans UA159
ComponentsPutative Hit-like protein involved in cell-cycle regulation
KeywordsCELL CYCLE / Hit-like protein / cell-cycle regulation
Function / homology
Function and homology information


catalytic activity / metal ion binding
Similarity search - Function
HINT family / Histidine triad (HIT) protein / HIT domain / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative Hit-like protein involved in cell-cycle regulation
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsSu, X.-D. / Ye, Z.Y. / Liu, X.
CitationJournal: TO BE PUBLISHED
Title: The Crystal Structure of SMU.412c from Streptococcus mutans UA159
Authors: Su, X.-D. / Ye, Z.Y. / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_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_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

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Assembly

Deposited unit
A: Putative Hit-like protein involved in cell-cycle regulation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2544
Polymers19,1431
Non-polymers1113
Water1,08160
1
A: Putative Hit-like protein involved in cell-cycle regulation
hetero molecules

A: Putative Hit-like protein involved in cell-cycle regulation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5088
Polymers38,2852
Non-polymers2236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5900 Å2
ΔGint-48 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.348, 53.348, 141.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative Hit-like protein involved in cell-cycle regulation / smu.412c


Mass: 19142.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: smu.412c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DVQ8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 53.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.8M Sodium acetate trihydrate pH7.0, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.699→50 Å / Num. all: 23363 / Num. obs: 23340 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 21.62 Å2
Reflection shellResolution: 1.699→1.76 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y23

1y23


Resolution: 1.699→35.274 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.853 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 20.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2129 2000 8.58 %
Rwork0.1879 21313 -
obs0.1901 23313 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.804 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 95.83 Å2 / Biso mean: 28.933 Å2 / Biso min: 12.75 Å2
Baniso -1Baniso -2Baniso -3
1-4.901 Å20 Å2-0 Å2
2--4.901 Å20 Å2
3----9.801 Å2
Refinement stepCycle: LAST / Resolution: 1.699→35.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1188 0 3 60 1251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0211207
X-RAY DIFFRACTIONf_angle_d1.8751631
X-RAY DIFFRACTIONf_dihedral_angle_d18.476434
X-RAY DIFFRACTIONf_chiral_restr0.154188
X-RAY DIFFRACTIONf_plane_restr0.01216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6992-1.74170.28161390.22211480X-RAY DIFFRACTION100
1.7417-1.78880.24211410.19431501X-RAY DIFFRACTION100
1.7888-1.84140.23291390.18671490X-RAY DIFFRACTION100
1.8414-1.90080.22571390.18791478X-RAY DIFFRACTION100
1.9008-1.96880.2091400.17741489X-RAY DIFFRACTION100
1.9688-2.04760.21251410.1781501X-RAY DIFFRACTION100
2.0476-2.14080.21431410.16881508X-RAY DIFFRACTION100
2.1408-2.25360.19921420.17261513X-RAY DIFFRACTION100
2.2536-2.39480.22081420.18041510X-RAY DIFFRACTION100
2.3948-2.57960.19171410.17661503X-RAY DIFFRACTION100
2.5796-2.83910.24491440.19521541X-RAY DIFFRACTION100
2.8391-3.24970.22741450.20191538X-RAY DIFFRACTION100
3.2497-4.09330.1861490.16931585X-RAY DIFFRACTION100
4.0933-35.28180.19781570.18841676X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -9.6919 Å / Origin y: -10.3415 Å / Origin z: -6.3348 Å
111213212223313233
T0.0868 Å2-0.0103 Å2-0.0011 Å2-0.133 Å2-0.0052 Å2--0.1324 Å2
L0.4763 °2-0.098 °2-0.2148 °2-0.5916 °20.2291 °2--2.5144 °2
S0.0003 Å °0.0917 Å °0.023 Å °-0.074 Å °-0.0025 Å °-0.0197 Å °-0.155 Å °0.1644 Å °0.0037 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-20 - 138
2X-RAY DIFFRACTION1allA1 - 140
3X-RAY DIFFRACTION1allA1 - 142
4X-RAY DIFFRACTION1allA1 - 206

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