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- PDB-3bgk: The crystal structure of hypothetic protein SMU.573 from Streptoc... -

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Basic information

Entry
Database: PDB / ID: 3bgk
TitleThe crystal structure of hypothetic protein SMU.573 from Streptococcus mutans
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / alpha/beta three layer sandwich
Function / homology
Function and homology information


ADP-dependent NAD(P)H-hydrate dehydratase / ADP-dependent NAD(P)H-hydrate dehydratase activity / nicotinamide nucleotide metabolic process / ATP binding
Similarity search - Function
Carbohydrate kinase, predicted, conserved site / YjeF C-terminal domain signature 2. / ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase / Carbohydrate kinase / YjeF C-terminal domain profile. / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / ADP-dependent (S)-NAD(P)H-hydrate dehydratase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SAD / MAD / Resolution: 2.5 Å
AuthorsLiang, Y.H. / Zhou, Y.F. / Yang, C. / Su, X.D.
CitationJournal: To be Published
Title: The crystal structure of Streptococcus mutans protein SMU.573 solved from the anomalous signal measured with in-house chromium radiation
Authors: Liang, Y.H. / Zhou, Y.F. / Li, L.F. / Su, X.D. / Yang, C.
History
DepositionNov 26, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 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 / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _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_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_conn.ptnr2_label_seq_id / _struct_conn_type.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2303
Polymers34,0961
Non-polymers1342
Water30617
1
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,92012
Polymers136,3834
Non-polymers5368
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.527, 96.527, 56.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Putative uncharacterized protein / SMU.573


Mass: 34095.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU.573 / Plasmid: pET-28a (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8DVC0
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.92 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.49M sodium phosphate monobasic monohydrate, 0.91M Potassium phosphate dibasic, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 2.2909 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 20, 2007 / Details: mirrors
RadiationMonochromator: multilayers optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.2909 Å / Relative weight: 1
ReflectionRedundancy: 10 % / Av σ(I) over netI: 32.1 / Number: 93650 / Rmerge(I) obs: 0.051 / Χ2: 1.1 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 9331 / % possible obs: 80.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955099.110.0531.0712.3
3.934.9599.510.0471.04312.2
3.443.9394.710.0481.1038.9
3.123.449710.0491.11211.5
2.93.1210010.0551.04912
2.732.999.910.061.18311.7
2.592.7385.510.0711.2627.5
2.482.5966.910.0780.9186.1
2.382.4843.810.091.0784
2.32.3813.110.0991.1642.3
ReflectionResolution: 2.5→25 Å / Num. obs: 8542 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.86 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 29.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 20.4 / Num. unique all: 629 / Rsym value: 0.078 / % possible all: 69.7

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Phasing

PhasingMethod: MAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1S14.9030.3530.5290.2790.801
2S28.5280.3220.3850.4641.018
3S35.2620.3010.4520.4131.051
4S42.8650.2960.5330.3971.186
5S40.5260.2780.4110.6070.97
6S43.6970.2470.420.0570.909
7S24.9540.3520.60.0930.595
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 9331
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.64-10045.20.793503
5.24-6.6448.60.826513
4.56-5.2444.80.834515
4.13-4.5645.90.841509
3.82-4.1354.80.81506
3.59-3.8251.30.798511
3.39-3.5952.50.772505
3.25-3.3950.40.822511
3.12-3.2549.40.811511
3.02-3.12520.785510
2.92-3.02560.755513
2.84-2.9251.90.771519
2.76-2.8451.60.767508
2.7-2.7655.20.788506
2.62-2.762.70.707509
2.55-2.6260.60.663511
2.48-2.5570.20.624503
2.32-2.4872.90.549668

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.869 / SU B: 9.284 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.256 413 4.8 %RANDOM
Rwork0.208 ---
obs0.21 8521 93.98 %-
all-10130 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.225 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2---0.99 Å20 Å2
3---1.98 Å2
Refine analyzeLuzzati coordinate error obs: 0.317 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 6 17 2043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222062
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9642805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1035274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09124.78971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45915327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.484156
X-RAY DIFFRACTIONr_chiral_restr0.0670.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021512
X-RAY DIFFRACTIONr_nbd_refined0.1960.2974
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.267
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.25
X-RAY DIFFRACTIONr_mcbond_it0.4151.51362
X-RAY DIFFRACTIONr_mcangle_it0.7822173
X-RAY DIFFRACTIONr_scbond_it1.0173706
X-RAY DIFFRACTIONr_scangle_it1.6144.5632
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 26 -
Rwork0.294 426 -
all-452 -
obs-426 67.46 %

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