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- PDB-1o50: Crystal structure of a cbs domain-containing protein (tm0935) fro... -

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Basic information

Entry
Database: PDB / ID: 1o50
TitleCrystal structure of a cbs domain-containing protein (tm0935) from thermotoga maritima at 1.87 A resolution
ComponentsCBS domain-containing predicted protein TM0935
KeywordsTRANSFERASE / Cbs-domain pair fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


: / 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
CBS domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.87 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a tandem cystathionine-beta-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 A resolution
Authors: Miller, M.D. / Schwarzenbacher, R. / von Delft, F. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / ...Authors: Miller, M.D. / Schwarzenbacher, R. / von Delft, F. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Levin, I. / McMullan, D. / McPhillips, T.M. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Robb, A. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionJul 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBS domain-containing predicted protein TM0935


Theoretical massNumber of molelcules
Total (without water)18,0401
Polymers18,0401
Non-polymers00
Water3,855214
1
A: CBS domain-containing predicted protein TM0935

A: CBS domain-containing predicted protein TM0935


Theoretical massNumber of molelcules
Total (without water)36,0802
Polymers36,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4430 Å2
ΔGint-42 kcal/mol
Surface area13400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)45.169, 45.169, 177.196
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 CBS domain-containing predicted protein TM0935


Mass: 18040.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0935 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X033
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.448.27
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop6crystal 1: 20% PEG-6000, 0.1M MES pH 6.0, 1M LiCl, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop6.6crystal 2: 0.2M ammonium formate, 20% PEG-3350, pH 6.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.2 Mammonium formate1reservoir
220 %PEG33501reservoirpH6.6
320 mMTris1droppH7.9
4150 mM1dropNaCl
50.25 mMTCEP1drop
624 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL9-110.97001
SYNCHROTRONSSRL BL11-120.97932, 0.90497
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJun 3, 2001flat mirror
ADSC QUANTUM 3152CCDDec 12, 2002flat mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(311) bent monochromatorSINGLE WAVELENGTHMx-ray1
2single crystal Si(311) bent monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.970011
20.979321
30.904971
ReflectionResolution: 1.83→31.63 Å / Num. all: 16963 / Num. obs: 16963 / % possible obs: 99 % / Redundancy: 3.2 % / Biso Wilson estimate: 32.45 Å2 / Rsym value: 0.072 / Net I/σ(I): 10.5
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 1130 / Rsym value: 0.62 / % possible all: 90.6
Reflection
*PLUS
Highest resolution: 1.83 Å / Num. measured all: 54281 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 90.6 % / Rmerge(I) obs: 0.622

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
RESOLVEmodel building
REFMACrefinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.87→31.43 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.887 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. ADDITIONAL N-TERMINAL HIS-TAG RESIDUES INDICATED BY CONTINUOUS BUT UNINTERPRETABLE DENSITY, AND WAS MODELED BY WATERS. 2. PROMINENT DENSITY AT MISSING RESIDUE A70 WAS MODELED AS WATER ...Details: 1. ADDITIONAL N-TERMINAL HIS-TAG RESIDUES INDICATED BY CONTINUOUS BUT UNINTERPRETABLE DENSITY, AND WAS MODELED BY WATERS. 2. PROMINENT DENSITY AT MISSING RESIDUE A70 WAS MODELED AS WATER CHAIN. 3. PROMINENT CONTINUOUS DENSITY AROUND RESIDUE A29 WAS MODELED AS WATER CHAIN. 4. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25495 813 5.1 %RANDOM
Rwork0.19113 ---
obs0.19435 15161 99.41 %-
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: 32.331 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.87→31.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 0 214 1338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221153
X-RAY DIFFRACTIONr_bond_other_d0.0020.021108
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9841558
X-RAY DIFFRACTIONr_angle_other_deg0.88232592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3315139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21725.62548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82515228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.069154
X-RAY DIFFRACTIONr_chiral_restr0.10.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021219
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02192
X-RAY DIFFRACTIONr_nbd_refined0.2080.2235
X-RAY DIFFRACTIONr_nbd_other0.2330.21271
X-RAY DIFFRACTIONr_nbtor_other0.0850.2658
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2134
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.216
X-RAY DIFFRACTIONr_mcbond_it0.7991.5708
X-RAY DIFFRACTIONr_mcangle_it1.37221163
X-RAY DIFFRACTIONr_scbond_it2.1233445
X-RAY DIFFRACTIONr_scangle_it3.4094.5395
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 65 5.73 %
Rwork0.339 1069 -
Refinement TLS params.Method: refined / Origin x: 19.361 Å / Origin y: 6.083 Å / Origin z: 90.821 Å
111213212223313233
T-0.2129 Å2-0.0294 Å20.0304 Å2--0.2602 Å20.0058 Å2---0.0525 Å2
L0.6858 °2-0.3753 °2-0.0639 °2-0.9229 °2-0.3208 °2--5.5461 °2
S-0.057 Å °0.0749 Å °-0.0466 Å °0.0069 Å °-0.0597 Å °-0.0489 Å °0.5621 Å °0.4261 Å °0.1167 Å °
Refinement TLS groupSelection: ALL
Software
*PLUS
Name: REFMAC / Version: 5.1.9999 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 15974 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.55
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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