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- PDB-1j6r: Crystal structure of Activation (AdoMet binding) domain of Methio... -

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Basic information

Entry
Database: PDB / ID: 1j6r
TitleCrystal structure of Activation (AdoMet binding) domain of Methionine synthase (TM0269) from Thermotoga maritima at 2.2 A resolution
ComponentsMETHIONINE SYNTHASE
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / TM0269 / ACTIVATION (ADOMET BINDING) DOMAIN OF METHIONINE SYNTHASE / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homologyNADH Oxidase - #40 / S-adenosyl-L-methionine dependent methionine synthase, predicted / Vitamin B12-dependent methionine synthase, activation domain superfamily / methionine synthase activity / NADH Oxidase / 3-Layer(aba) Sandwich / Alpha Beta / Methionine synthase
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Activation (AdoMet binding) domain of Methionine synthase (TM0269) from Thermotoga maritima at 2.2 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Advisory / Data collection / Database references
Category: pdbx_database_related / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Revision 1.4Jan 25, 2023Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5May 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: METHIONINE SYNTHASE
B: METHIONINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)48,7682
Polymers48,7682
Non-polymers00
Water1,856103
1
A: METHIONINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)24,3841
Polymers24,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: METHIONINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)24,3841
Polymers24,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.396, 60.740, 81.574
Angle α, β, γ (deg.)90.00, 99.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein METHIONINE SYNTHASE


Mass: 24383.975 Da / Num. of mol.: 2 / Fragment: ACTIVATION (ADOMET BINDING) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0269 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYA6, methionine synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 293 K / pH: 7
Details: 2.4 M Ammonium Sulfate; 0.1 M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.979029
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.9790291
ReflectionResolution: 2.25→36.22 Å / Num. obs: 27922 / % possible obs: 90.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 43.3 Å2 / Rsym value: 0.048 / Net I/σ(I): 14
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.344 / % possible all: 93.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4data reduction
RESOLVEmodel building
CNSrefinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→36.22 Å / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH AND HUBER
Details: DISORDERED SIDECHAINS: CHAIN A: 45, 52,72,76,154,170, 179,180,181,197; CHAIN B: 30,31,34,45,52,72, 76, 86,145,154,163,164,170,178,181,197 DISORDERED RESIDUES: CHAIN A: 177,178 CHAIN B: ...Details: DISORDERED SIDECHAINS: CHAIN A: 45, 52,72,76,154,170, 179,180,181,197; CHAIN B: 30,31,34,45,52,72, 76, 86,145,154,163,164,170,178,181,197 DISORDERED RESIDUES: CHAIN A: 177,178 CHAIN B: 179,180. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1500 5.1 %RANDOM
Rwork0.251 ---
obs0.251 27922 99.9 %-
Solvent computationSolvent model: BULK SOLVENT MODELLING / Bsol: 322.79 Å2 / ksol: 0.9 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å2-0.33 Å2
2--2.81 Å20 Å2
3----1.75 Å2
Refine analyzeLuzzati coordinate error obs: 0.59 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.3→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 0 103 3249
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4171.5
X-RAY DIFFRACTIONc_mcangle_it2.5272
X-RAY DIFFRACTIONc_scbond_it1.2522
X-RAY DIFFRACTIONc_scangle_it2.2012.5
LS refinement shellResolution: 2.3→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 119 5 %
Rwork0.325 2076 -
obs--96 %

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