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- PDB-1vr9: CRYSTAL STRUCTURE OF A CBS DOMAIN PAIR/ACT DOMAIN PROTEIN (TM0892... -

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Basic information

Entry
Database: PDB / ID: 1vr9
TitleCRYSTAL STRUCTURE OF A CBS DOMAIN PAIR/ACT DOMAIN PROTEIN (TM0892) FROM THERMOTOGA MARITIMA AT 1.70 A RESOLUTION
ComponentsCBS domain protein/ACT domain protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


magnesium ion transmembrane transporter activity / membrane
Similarity search - Function
Ubiquitin-like (UB roll) - #750 / CBS domain Like - #20 / CBS domain Like / Magnesium transporter MgtE / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily ...Ubiquitin-like (UB roll) - #750 / CBS domain Like - #20 / CBS domain Like / Magnesium transporter MgtE / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CBS domain containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of CBS domain protein/ACT domain protein (TM0892) from Thermotoga maritima at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CBS domain protein/ACT domain protein
B: CBS domain protein/ACT domain protein


Theoretical massNumber of molelcules
Total (without water)49,3312
Polymers49,3312
Non-polymers00
Water4,360242
1
A: CBS domain protein/ACT domain protein


Theoretical massNumber of molelcules
Total (without water)24,6651
Polymers24,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CBS domain protein/ACT domain protein


Theoretical massNumber of molelcules
Total (without water)24,6651
Polymers24,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)228.040, 52.647, 44.161
Angle α, β, γ (deg.)90.00, 100.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CBS domain protein/ACT domain protein


Mass: 24665.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0892 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZZ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.6453.45
22.6853.7DATA FROM A SE-MET CONTAINING CRYSTAL IN SPACEGROUP I222 WAS USED FOR THE MAD PHASING EXPERIMENTS AT 2.0 ANGSTROMS RESOLUTION. THIS MAD STRUCTURE WAS USED AS A MOLECULAR REPLACEMENT MODEL TO PHASE THE STRUCTURE OF A SECOND CRYSTAL IN SPACEGROUP C2 THAT WAS REFINED TO A RESOLUTION OF 1.70A.
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop7.520.0% PEG-8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop7.520.0% PEG-10000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.110.99187
SYNCHROTRONALS 8.3.120.979741, 1.019859
Detector
TypeIDDetectorDate
ADSC1CCDJan 21, 2005
ADSC2CCDJan 6, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Double Crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.991871
20.9797411
31.0198591
ReflectionResolution: 1.7→37.81 Å / Num. obs: 45259 / % possible obs: 81.56 % / Redundancy: 3.16 % / Biso Wilson estimate: 29.22 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 20.66
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.96 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.45 / Num. unique all: 4044 / % possible all: 73.13

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 1.7→37.81 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.895 / SU B: 3.434 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. IT WAS NOT POSSIBLE TO TRACE RESIDUES 122-201 IN EACH CHAIN. PFAM ANALYSIS OF THE SEQUENCE INDICATES THAT THIS REGION IS COMPOSED OF ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. IT WAS NOT POSSIBLE TO TRACE RESIDUES 122-201 IN EACH CHAIN. PFAM ANALYSIS OF THE SEQUENCE INDICATES THAT THIS REGION IS COMPOSED OF AN ACT DOMAIN. MASS SPECTROSCOPY INDICATES THAT THE PROTEIN IS COMPLETE, SUGGESTING THAT THIS REGION IS DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.26992 2336 5.1 %RANDOM
Rwork0.24563 ---
obs0.24687 43645 80.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.729 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.31 Å2
2---0.8 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 0 242 2228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222077
X-RAY DIFFRACTIONr_bond_other_d0.0020.021907
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.9612798
X-RAY DIFFRACTIONr_angle_other_deg0.88234453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8245240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95524.386114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38315404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8561516
X-RAY DIFFRACTIONr_chiral_restr0.0750.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022254
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02416
X-RAY DIFFRACTIONr_nbd_refined0.2120.2467
X-RAY DIFFRACTIONr_nbd_other0.1760.22039
X-RAY DIFFRACTIONr_nbtor_other0.0820.21121
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.215
X-RAY DIFFRACTIONr_mcbond_it1.121.51519
X-RAY DIFFRACTIONr_mcbond_other0.2251.5486
X-RAY DIFFRACTIONr_mcangle_it1.23621981
X-RAY DIFFRACTIONr_scbond_it2.3113942
X-RAY DIFFRACTIONr_scangle_it3.2944.5817
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2985
LS refinement shellResolution: 1.697→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 143 5.23 %
Rwork0.214 2591 -
obs--65.72 %
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)
13.0152-0.66680.84351.8768-0.55712.3132-0.04930.04050.08360.0461-0.031-0.1448-0.16250.00280.0804-0.0308-0.00370.0107-0.1773-0.0061-0.1874-44.768-0.248-12.92
23.921.0444-0.50861.8986-0.12021.5924-0.0338-0.0984-0.09550.0481-0.0468-0.1350.14910.00470.0806-0.03730.00370.0376-0.1689-0.0032-0.1714-46.332-24.153-5.32
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 121 / Label seq-ID: 13 - 133

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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