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- PDB-2f2g: X-Ray Structure of Gene Product From Arabidopsis Thaliana AT3G16990 -

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Basic information

Entry
Database: PDB / ID: 2f2g
TitleX-Ray Structure of Gene Product From Arabidopsis Thaliana AT3G16990
ComponentsSEED MATURATION PROTEIN PM36 HOMOLOG
KeywordsPLANT PROTEIN / TENA_THI-4 DOMAIN / TENA/THI-4/PQQC FAMILY / AT3G16990 / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / CENTER FOREUKARYOTIC STRUCTURAL GENOMICS / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


aminopyrimidine aminohydrolase / thiaminase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
Similarity search - Function
TenA_E protein / : / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE / Bifunctional TENA-E protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.1 Å
AuthorsWesenberg, G.W. / Smith, D.W. / Phillips Jr., G.N. / Johnson, K.A. / Bitto, E. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of gene locus At3g16990 from Arabidopsis thaliana
Authors: Blommel, P.G. / Smith, D.W. / Bingman, C.A. / Dyer, D.H. / Rayment, I. / Holden, H.M. / Fox, B.G. / Phillips Jr., G.N.
History
DepositionNov 16, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionDec 13, 2005ID: 1Q4M
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEED MATURATION PROTEIN PM36 HOMOLOG
B: SEED MATURATION PROTEIN PM36 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3288
Polymers50,6652
Non-polymers6636
Water7,692427
1
A: SEED MATURATION PROTEIN PM36 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5683
Polymers25,3331
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SEED MATURATION PROTEIN PM36 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7605
Polymers25,3331
Non-polymers4274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.700, 62.700, 287.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYALAALAAA5 - 215 - 21
21GLYGLYALAALABB5 - 215 - 21
32SERSERHISHISAA38 - 14938 - 149
42SERSERHISHISBB38 - 14938 - 149
53GLYGLYMSEMSEAA163 - 216163 - 216
63GLYGLYMSEMSEBB163 - 216163 - 216

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Components

#1: Protein SEED MATURATION PROTEIN PM36 HOMOLOG / protein At3g16990


Mass: 25332.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g16990 / Plasmid: PVP13 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9ASY9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HMH / 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE


Mass: 139.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9N3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.78 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein solution (15 mg/ml protein, 0.025 M sodium chloride, 0.10 M Tris pH 7.5) mixed in a 1:1 ratio with the well solution (0.055 M sodium acetate pH 4.5, 1.05 M ammonium sulfate), ...Details: Protein solution (15 mg/ml protein, 0.025 M sodium chloride, 0.10 M Tris pH 7.5) mixed in a 1:1 ratio with the well solution (0.055 M sodium acetate pH 4.5, 1.05 M ammonium sulfate), temperature 277 K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.97912 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2003 / Details: Bent cylindrical Si-mirror (Rh coating)
RadiationMonochromator: Diamond (111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.08→43.81 Å / Num. obs: 30515 / % possible obs: 84.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 22.303
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.08-2.156.10.266.376144.8
2.15-2.2470.195155.7
2.24-2.347.70.175168
2.34-2.478.40.125188.2
2.47-2.6210.30.121199.4
2.62-2.8210.80.086199.7
2.82-3.1110.70.071199.7
3.11-3.5610.60.057199.6
3.56-4.4810.30.05199.4
4.48-509.30.058192

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.5 Å / D res low: 25 Å / FOM : 0.47 / Reflection: 20370
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se38.110.4330.1120.1051.612
2Se35.0660.8220.0690.0861.346
3Se56.1350.6920.210.0731.525
4Se34.1160.6640.6920.0981.097
5Se26.7140.6230.2210.1090.704
6Se41.9620.5620.4840.0780.815
7Se600.5290.9570.091.547
Phasing MAD shell
Resolution (Å)FOM Reflection
8.74-250.42901
5.61-8.740.511776
4.41-5.610.52213
3.75-4.410.52563
3.32-3.750.482873
3.01-3.320.493144
2.77-3.010.463383
2.58-2.770.393517
Phasing dmFOM : 0.69 / FOM acentric: 0.73 / FOM centric: 0.5 / Reflection: 20370 / Reflection acentric: 16709 / Reflection centric: 3661
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-24.9210.770.890.59769458311
4.5-7.10.820.890.6228562127729
3.6-4.50.830.880.6535162813703
3.1-3.60.750.790.5334612884577
2.7-3.10.620.670.3660945213881
2.5-2.70.470.50.2536743214460

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.02phasing
RESOLVE2.02phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.701data extraction
MAR345data collection
RefinementMethod to determine structure: SAD / Resolution: 2.1→43.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.176 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SELENIUM C COEFFICIENT FOR STRUCTURE FACTOR CALCULATION SET TO -9.00, MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING.
RfactorNum. reflection% reflectionSelection details
Rfree0.23355 1519 5.1 %RANDOM
Rwork0.16979 ---
obs0.17306 28535 86.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.599 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 40 427 3869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223545
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9364805
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8895423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48923.52179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38715586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.871529
X-RAY DIFFRACTIONr_chiral_restr0.1020.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022707
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.21779
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22513
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2339
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.2111
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.69422169
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.59543408
X-RAY DIFFRACTIONr_scbond_it4.89161603
X-RAY DIFFRACTIONr_scangle_it6.66781397
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: 1452 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.50.5
medium thermal1.852
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 58 -
Rwork0.165 1151 -
obs--48.05 %
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)
10.45120.01620.01880.79020.46061.3281-0.0234-0.0361-0.0234-0.13920.0715-0.0440.0080.127-0.04810.03220.0112-0.0279-0.0898-0.003-0.03232.68149.76849.982
21.6774-0.65460.62061.54350.10220.32170.0243-0.1379-0.05290.17020.03050.00580.0217-0.092-0.05480.11680.001-0.0309-0.1036-0.0005-0.08346.59423.02750.127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 2195 - 219
2X-RAY DIFFRACTION2BB4 - 2194 - 219

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