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- PDB-1vkf: CRYSTAL STRUCTURE OF A GLYCEROL UPTAKE OPERON ANTITERMINATOR-RELA... -

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Basic information

Entry
Database: PDB / ID: 1vkf
TitleCRYSTAL STRUCTURE OF A GLYCEROL UPTAKE OPERON ANTITERMINATOR-RELATED PROTEIN (TM1436) FROM THERMOTOGA MARITIMA MSB8 AT 1.65 A RESOLUTION
Componentsglycerol uptake operon antiterminator-related protein
KeywordsTRANSCRIPTION / GLYCEROL UPTAKE OPERON ANTITERMINATOR-RELATED PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


glycerol metabolic process / transcription antitermination factor activity, RNA binding
Similarity search - Function
Glycerol uptake operon antiterminator / Glycerol-3-phosphate responsive antiterminator / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / PHOSPHATE ION / Glycerol uptake operon antiterminator-related protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Glycerol uptake operon antiterminator-related protein (TM1436) from Thermotoga maritima at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycerol uptake operon antiterminator-related protein
B: glycerol uptake operon antiterminator-related protein
C: glycerol uptake operon antiterminator-related protein
D: glycerol uptake operon antiterminator-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5648
Polymers83,8924
Non-polymers6714
Water7,044391
1
A: glycerol uptake operon antiterminator-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1652
Polymers20,9731
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glycerol uptake operon antiterminator-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0682
Polymers20,9731
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: glycerol uptake operon antiterminator-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1652
Polymers20,9731
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: glycerol uptake operon antiterminator-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1652
Polymers20,9731
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.527, 138.783, 160.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: MSE / End label comp-ID: MSE / Refine code: 6 / Auth seq-ID: 1 - 172 / Label seq-ID: 13 - 184

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
glycerol uptake operon antiterminator-related protein


Mass: 20973.043 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1436 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1F0
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.94 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.5
Details: Citrate pH 5.5, 50% PEG-200, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.953693
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2004
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953693 Å / Relative weight: 1
ReflectionResolution: 1.65→80.31 Å / Num. obs: 110006 / % possible obs: 97.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 33.7 Å2 / Rsym value: 0.074 / Net I/σ(I): 13.3
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 6833 / Rsym value: 0.576 / % possible all: 82.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→72.19 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.105 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21126 5519 5 %RANDOM
Rwork0.18517 ---
obs0.18649 104433 97.1 %-
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: 18.094 Å2
Baniso -1Baniso -2Baniso -3
1--2.35 Å20 Å20 Å2
2---0.84 Å20 Å2
3---3.19 Å2
Refinement stepCycle: LAST / Resolution: 1.65→72.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5246 0 44 391 5681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225406
X-RAY DIFFRACTIONr_bond_other_d0.0050.025292
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9847311
X-RAY DIFFRACTIONr_angle_other_deg0.836312272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2315694
X-RAY DIFFRACTIONr_chiral_restr0.0950.2874
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025886
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021007
X-RAY DIFFRACTIONr_nbd_refined0.2140.2940
X-RAY DIFFRACTIONr_nbd_other0.2390.26079
X-RAY DIFFRACTIONr_nbtor_other0.0850.23422
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.223
X-RAY DIFFRACTIONr_mcbond_it2.21633437
X-RAY DIFFRACTIONr_mcangle_it3.34155557
X-RAY DIFFRACTIONr_scbond_it5.40581969
X-RAY DIFFRACTIONr_scangle_it8.002111754
Refine LS restraints NCS

Ens-ID: 1 / Number: 2501 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.545
2Bloose positional0.585
3Cloose positional0.455
4Dloose positional0.725
1Aloose thermal4.5510
2Bloose thermal4.0910
3Cloose thermal3.7310
4Dloose thermal5.7910
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 318 4.66 %
Rwork0.329 6503 -
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)
11.50430.5467-0.10140.7312-0.04720.38060.117-0.1054-0.02420.1157-0.06050.0786-0.04980.0137-0.05640.17370.00180.00510.09060.02170.106165.647937.448644.8019
21.1126-0.3885-0.18261.1926-0.02080.41690.05640.11060.0198-0.128-0.0631-0.00020.007-0.06350.00670.13490.00630.00940.08960.00370.162365.5888.885536.6448
31.7896-0.28980.19650.748-0.94672.05290.03320.1614-0.2935-0.03540.06210.12320.1936-0.2129-0.09530.1002-0.02060.0080.223-0.04270.059688.0519-10.910510.4689
41.3337-0.25090.56821.7922-1.00982.64780.00730.39990.31920.0415-0.3259-0.224-0.03760.71020.31870.09890.01160.00370.38850.17920.092141.1733-4.729914.466
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 172 / Label seq-ID: 13 - 184

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD

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