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- PDB-3ghd: Crystal structure of a cystathionine beta-synthase domain protein... -

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Basic information

Entry
Database: PDB / ID: 3ghd
TitleCrystal structure of a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain
Componentsa cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain
KeywordsNucleotide binding protein / Metal binding protein / PF1953 / APC40009 / cystathionine beta-synthase domain protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / METAL BINDIN
Function / homologyCBS domain Like - #20 / CBS domain Like / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Alpha-Beta Complex / Alpha Beta / Inosine-5'-monophosphate dehydrogenase related protein II
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsDong, A. / Xu, X. / Chruszcz, M. / Brown, G. / Proudfoot, M. / Edwards, A.M. / Joachimiak, A. / Minor, W. / Savchenko, A. / Yaleunin, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain
Authors: Dong, A. / Xu, X. / Chruszcz, M. / Brown, G. / Proudfoot, M. / Edwards, A.M. / Joachimiak, A. / Minor, W. / Savchenko, A. / Yaleunin, A.
History
DepositionMar 3, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionMar 31, 2009ID: 3FIO
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 4, 2012Group: Structure summary
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain
B: a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain


Theoretical massNumber of molelcules
Total (without water)15,4942
Polymers15,4942
Non-polymers00
Water2,018112
1
A: a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain
B: a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain

A: a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain
B: a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain


Theoretical massNumber of molelcules
Total (without water)30,9874
Polymers30,9874
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area4700 Å2
ΔGint-33 kcal/mol
Surface area13680 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-8 kcal/mol
Surface area7930 Å2
MethodPISA
3
B: a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain

B: a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain


Theoretical massNumber of molelcules
Total (without water)15,4942
Polymers15,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area1550 Å2
ΔGint-13 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.153, 73.162, 35.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

#1: Protein a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain


Mass: 7746.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PET DERIVATIVE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)DERIVATIVE / References: UniProt: Q8TZN4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE PROTEIN WAS CRYSTALLIZED BY IN SITU PROTEOLYSIS METHOD AND THE EXACT ...AUTHORS STATE THAT THE PROTEIN WAS CRYSTALLIZED BY IN SITU PROTEOLYSIS METHOD AND THE EXACT SEQUENCE WENT INTO THE CRYSTAL WAS NOT DETERMINED. THE PROTEIN WAS MIXED WITH 100:1(W/W) WITH CHYMOTRYPSIN IMMEDIATELY PRIOR TO CRYSTALLIZATION TRIAL. THE FULL SEQUENCE BEFORE PROTEOLYSIS WAS MGSSHHHHHHSSGRENLYFQGMAQKILVEQVVKRKAIVVQPKDTVDRVAKILSRNKAG SAVVMEGDEILGVVTERDILDKVVAKGKNPKEVKVEEIMTKNPVKIEYDYDIEDVIEL MTEKGVRRVLVTKFGKPIGFVTAADILAALASHNHEEEEEEREEESEVYGICEVCGQY GALYKVYHEGRELWVCETCKDLIEGR

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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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium Chloride,20%PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97941 Å
DetectorType: unsupported-m300 / Detector: CCD / Date: Oct 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 11994 / Num. obs: 11994 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 14.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 5.84 / Num. unique all: 798 / Rsym value: 0.202 / % possible all: 61

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
RESOLVEmodel building
REFMAC5.5.0062refinement
Coot0.3.3model building
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.81→31.77 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.635 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.15 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOMIC B-FACTORS ARE RESIDUALS FROM TLS REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.24108 596 5 %RANDOM
Rwork0.19229 ---
all0.19455 11368 --
obs0.19455 11368 89.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.171 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2--1.49 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.81→31.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 0 112 1139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221031
X-RAY DIFFRACTIONr_bond_other_d0.0010.02685
X-RAY DIFFRACTIONr_angle_refined_deg1.80721393
X-RAY DIFFRACTIONr_angle_other_deg1.05631724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.745138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85228.12532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52815206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.451153
X-RAY DIFFRACTIONr_chiral_restr0.1120.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211103
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02144
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8531.5696
X-RAY DIFFRACTIONr_mcbond_other0.2711.5280
X-RAY DIFFRACTIONr_mcangle_it1.37521137
X-RAY DIFFRACTIONr_scbond_it2.6773335
X-RAY DIFFRACTIONr_scangle_it4.2934.5256
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 755 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.340.5
medium thermal0.862
LS refinement shellResolution: 1.805→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 31 -
Rwork0.196 535 -
obs--58.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.35790.623-1.31320.733-0.41094.28750.1162-0.06970.29150.04230.06920.0717-0.2888-0.5035-0.18550.13780.09450.00740.1288-0.00860.170236.5249.31914.28
21.6668-0.8807-0.91621.3447-0.05061.92160.03510.11520.3333-0.00110.0622-0.0517-0.2702-0.1477-0.09730.1256-0.0040.00920.02770.02960.146151.3148.48-2.343
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 83
2X-RAY DIFFRACTION2B14 - 83

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