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- PDB-2rc3: Crystal structure of CBS domain, NE2398 -

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Basic information

Entry
Database: PDB / ID: 2rc3
TitleCrystal structure of CBS domain, NE2398
ComponentsCBS domain
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / CBS domain / in situ proteolysis / Br / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


CBS domain-containing protein CBSX3, CBS domain / : / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / CBS domain
Similarity search - Component
Biological speciesNitrosomonas europaea ATCC 19718 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsDong, A. / Xu, X. / Korniyenko, Y. / Yakunin, A. / Zheng, H. / Walker, J.R. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of CBS domain, NE2398.
Authors: Dong, A. / Xu, X. / Korniyenko, A. / Yakunin, A. / Zheng, H. / Walker, J.R. / Edwards, A.M. / Joachimiak, A. / Savchenko, A.
History
DepositionSep 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: CBS domain
B: CBS domain
C: CBS domain
D: CBS domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,44847
Polymers60,6794
Non-polymers5,77043
Water12,791710
1
A: CBS domain
D: CBS domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,34425
Polymers30,3392
Non-polymers3,00523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
MethodPISA
2
B: CBS domain
C: CBS domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,10422
Polymers30,3392
Non-polymers2,76520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.195, 95.641, 99.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein
CBS domain


Mass: 15169.631 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea ATCC 19718 (bacteria)
Species: Nitrosomonas europaea / Strain: IFO 14298 / Gene: NE2398 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q82SE2
#2: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 2.09 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1M Na(OAC) pH 5.2, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9197 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 67993 / Num. obs: 67993 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 7.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 1.57 / Num. unique all: 6501 / Rsym value: 0.682 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.923 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.097 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Programs COOT 1.0, ARP/wARP 6.1.1 have also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.23595 676 1 %RANDOM
Rwork0.18759 ---
all0.18807 66839 --
obs0.18807 66839 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.641 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2--0.34 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 215 710 4859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224167
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4222.0415656
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20725.556153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62515787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0041520
X-RAY DIFFRACTIONr_chiral_restr0.0820.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022900
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.22135
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22920
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2511
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.255
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8911.52624
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34224138
X-RAY DIFFRACTIONr_scbond_it1.93831685
X-RAY DIFFRACTIONr_scangle_it3.0784.51518
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 42 -
Rwork0.269 4566 -
obs--92.12 %

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