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- PDB-2rad: Crystal structure of the succinoglycan biosynthesis protein. Nort... -

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Basic information

Entry
Database: PDB / ID: 2rad
TitleCrystal structure of the succinoglycan biosynthesis protein. Northeast structural Genomics Consortium target BcR135
ComponentsSuccinoglycan biosynthesis protein
KeywordsBIOSYNTHETIC PROTEIN / NESG / BcR135 / Succinoglycan biosynthesis protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / UNKNOWN FUNCTION
Function / homology
Function and homology information


response to antibiotic / metal ion binding
Similarity search - Function
Biosynthetic Protein domain / EreA/ChaN-like, small alpha-beta sandwich / EreA-like; domain 2 / EreA/ChaN-like fold / EreA-like (biosynthetic domain) / Uncharacterised conserved protein UCP036794, erythromycin esterase-type / Erythromycin esterase / : / Erythromycin esterase / de novo design (two linked rop proteins) ...Biosynthetic Protein domain / EreA/ChaN-like, small alpha-beta sandwich / EreA-like; domain 2 / EreA/ChaN-like fold / EreA-like (biosynthetic domain) / Uncharacterised conserved protein UCP036794, erythromycin esterase-type / Erythromycin esterase / : / Erythromycin esterase / de novo design (two linked rop proteins) / Up-down Bundle / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Succinoglycan biosynthesis protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsKuzin, A.P. / Abashidze, M. / Seetharaman, J. / Wang, H. / Mao, L. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Wang, H. / Mao, L. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the succinoglycan biosynthesis protein.
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Wang, H. / Mao, L. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinoglycan biosynthesis protein
B: Succinoglycan biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)103,3422
Polymers103,3422
Non-polymers00
Water55831
1
A: Succinoglycan biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)51,6711
Polymers51,6711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Succinoglycan biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)51,6711
Polymers51,6711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.786, 54.187, 98.911
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Succinoglycan biosynthesis protein


Mass: 51671.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Species: Bacillus cereus / Strain: DSM 31 / Gene: BC_3120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81BN2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl pH 8.5, 18% PEG 3350, 25mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 12, 2007 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 45750 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.7 / % possible all: 79.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→19.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 128328.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: The Friedel pairs were used for phasing. Bulk solvent model was used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.281 3800 9.9 %RANDOM
Rwork0.209 ---
obs0.209 38513 82.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.6344 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 62.8 Å2
Baniso -1Baniso -2Baniso -3
1--25.33 Å20 Å27.51 Å2
2--21.71 Å20 Å2
3---3.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.75→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6475 0 0 31 6506
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 385 9.9 %
Rwork0.306 3495 -
obs--50 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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