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- PDB-1vm0: X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT2G34160 -

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Basic information

Entry
Database: PDB / ID: 1vm0
TitleX-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT2G34160
Componentsunknown protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / CESG / At2g34160 / Nitrate / PSI / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


rRNA processing / mRNA binding / endoplasmic reticulum / nucleus
Similarity search - Function
Uncharacterised conserved protein UCP030333, DNA/RNA-binding Alba-related / Alba-like domain / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NITRATE ION / Uncharacterized protein At2g34160
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsWesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be published
Title: X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT2G34160
Authors: Center for Eukaryotic Structural Genomics
History
DepositionAug 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_database_remark.text / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE PROBABLE BIOLOGICAL UNIT IS A TETRAMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: unknown protein
B: unknown protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0608
Polymers29,7342
Non-polymers3266
Water2,900161
1
A: unknown protein
B: unknown protein
hetero molecules

A: unknown protein
B: unknown protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,12116
Polymers59,4684
Non-polymers65212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9550 Å2
ΔGint-31 kcal/mol
Surface area18700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.785, 79.079, 43.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe putative biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -x+1, -y+1, z.)

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Components

#1: Protein unknown protein


Mass: 14867.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g34160 / Plasmid details: pQE derivative / Plasmid: pVP13-GW / Cell line (production host): B834-DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: O22969
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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 % sol: 29.24 %
Crystal growTemperature: 293 K / Method: batch / pH: 7
Details: protein 10 mg/ml, 18% PEG2K, potassium nitrate 0.200 M, MOPS 0.100 M, pH 7.0, Batch, temperature 293 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.97908,0.97931,0.97623
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 3, 2004 / Details: RH MIRROR
RadiationMonochromator: DIAMOND 111 MIRROR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979081
20.979311
30.976231
ReflectionResolution: 1.8→30 Å / Num. obs: 37012 / % possible obs: 99.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.068 / Χ2: 0.929 / Net I/σ(I): 14
Reflection shell

Mean I/σ(I) obs: 3.7 / Diffraction-ID: 1 / Redundancy: 3.8 %

Resolution (Å)Rmerge(I) obsNum. measured allΧ2% possible all
1.8-1.860.32935440.72495.7
1.86-1.940.27436920.79499.2
1.94-2.030.19837170.91299.6
2.03-2.130.1637150.99599.7
2.13-2.270.12437091.00999.9
2.27-2.440.10137101.022100
2.44-2.690.08437261.056100
2.69-3.080.06537290.961100
3.08-3.880.04337220.844100
3.88-300.03537480.90799.9

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 1.804 Å / D res low: 20 Å / FOM : 0.61 / Reflection: 19201
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
1110.97932.61-14.82
1120.97917.9-2.26
1130.97624.28-6.08
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
17.9750.4263.407SE19.90.35
253.364.5744.72SE22.80.29
30.1718.30618.174SE23.30.25
41.46924.67312.181SE230.28
540.00924.5059.67SE240.32
641.90318.2663.913SE18.30.2
Phasing MAD shell
Resolution (Å)FOM Reflection
6.36-200.821034
4.06-6.360.831683
3.19-4.060.82099
2.71-3.190.762435
2.4-2.710.72724
2.17-2.40.592945
2-2.170.463128
1.86-20.283153
Phasing dmFOM : 0.69 / FOM acentric: 0.69 / FOM centric: 0.68 / Reflection: 19306 / Reflection acentric: 16952 / Reflection centric: 2354
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.1-19.9320.940.940.88938646292
3.2-5.10.920.930.8927322240492
2.6-3.20.850.860.7833192882437
2.3-2.60.780.790.6633132939374
1.9-2.30.60.610.5157175209508
1.8-1.90.340.350.2932873036251

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefmac_5.1.24refinement
PDB_EXTRACT1data extraction
RefinementResolution: 1.8→29.361 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.174 / SU B: 2.186 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 1030 5.198 %RANDOM
Rwork0.1744 ---
all0.177 ---
obs0.17675 18785 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.158 Å20 Å20 Å2
2---0.165 Å20 Å2
3----0.993 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 0 18 161 1733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221581
X-RAY DIFFRACTIONr_bond_other_d0.0010.021502
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.9772115
X-RAY DIFFRACTIONr_angle_other_deg1.01933519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3785193
X-RAY DIFFRACTIONr_chiral_restr0.110.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021680
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02278
X-RAY DIFFRACTIONr_nbd_refined0.2640.2285
X-RAY DIFFRACTIONr_nbd_other0.2470.21718
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2761
X-RAY DIFFRACTIONr_nbtor_other0.0870.21008
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2115
X-RAY DIFFRACTIONMetal-ion: refined atoms0.1320.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3450.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.233
X-RAY DIFFRACTIONMetal-ion; symmetry: refined atoms0.1720.24
X-RAY DIFFRACTIONr_mcbond_it1.592988
X-RAY DIFFRACTIONr_mcbond_other0.3472391
X-RAY DIFFRACTIONr_mcangle_it3.01341584
X-RAY DIFFRACTIONr_mcangle_other1.34941334
X-RAY DIFFRACTIONr_scbond_it5.3276593
X-RAY DIFFRACTIONr_scbond_other1.28761111
X-RAY DIFFRACTIONr_scangle_it8.4688531
X-RAY DIFFRACTIONr_scangle_other3.77682185
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.799-1.84540.278650.2213421448
1.845-1.89590.218760.18513051395
1.896-1.95080.222800.16812801363
1.951-2.01070.189760.15212551336
2.011-2.07660.195670.14912241293
2.077-2.14930.185620.16211711235
2.149-2.23020.244470.16211591207
2.23-2.32110.197550.1511331189
2.321-2.42410.197710.15210431114
2.424-2.5420.236640.16110211085
2.542-2.67910.206550.1779541009
2.679-2.84110.207540.179937991
2.841-3.03650.209400.171866906
3.036-3.27870.206470.173813860
3.279-3.58990.213370.169768805
3.59-4.01080.188410.169687728
4.011-4.62580.214380.163605643
4.626-5.65210.263220.211542564
5.652-7.93770.428200.258420440
7.938-47.67310.368130.222260281

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