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- PDB-3emm: X-ray structure of protein from Arabidopsis thaliana AT1G79260 wi... -

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Basic information

Entry
Database: PDB / ID: 3emm
TitleX-ray structure of protein from Arabidopsis thaliana AT1G79260 with Bound Heme
ComponentsUncharacterized protein At1g79260
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HEME / Structural Genomics Functional Follow-up Study / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


Isomerases; Other isomerases / isomerase activity / metal ion binding / cytosol
Similarity search - Function
THAP4-like, heme-binding beta-barrel domain / Nitrobindin family / THAP4-like, heme-binding beta-barrel domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Peroxynitrite isomerase Rv2717c
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.358 Å
AuthorsBianchetti, C.M. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2010
Title: The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1.
Authors: Bianchetti, C.M. / Blouin, G.C. / Bitto, E. / Olson, J.S. / Phillips, G.N.
History
DepositionSep 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Uncharacterized protein At1g79260
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1873
Polymers18,5081
Non-polymers6792
Water4,558253
1
A: Uncharacterized protein At1g79260
hetero molecules

A: Uncharacterized protein At1g79260
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3736
Polymers37,0162
Non-polymers1,3574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4450 Å2
ΔGint-41 kcal/mol
Surface area14150 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.749, 79.732, 36.971
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Uncharacterized protein At1g79260


Mass: 18507.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g79260, YUP8H12R.14 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: O64527
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein Solution (16.5 mg/mL native protein [Heme was added in purification step], 0.050 M sodium chloride, 0.0003 M TCEP, 0.005 M MES pH 6.0) mixed in a 1:1 ratio with the Well Solution ...Details: Protein Solution (16.5 mg/mL native protein [Heme was added in purification step], 0.050 M sodium chloride, 0.0003 M TCEP, 0.005 M MES pH 6.0) mixed in a 1:1 ratio with the Well Solution (24% PEG 4K, 0.05 M BTP pH 7.0 ) Cryoprotected with 30% PEG 4K, 0.05 M BTP pH 7.0 and 15% ethylene glycol, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 19, 2008 / Details: Beryllium lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.358→50 Å / Num. obs: 37822 / % possible obs: 97.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.041 / Χ2: 0.967 / Net I/σ(I): 22.969
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.36-1.413.70.2365.07437280.95797.6
1.41-1.474.50.1938300.98399.8
1.47-1.534.70.14138240.98599.8
1.53-1.614.70.09938371.00199.5
1.61-1.714.80.07937921.06299.3
1.71-1.854.90.06738441.07199
1.85-2.034.90.04737951.03398.4
2.03-2.3350.04738340.93397.6
2.33-2.9350.04337960.92196.2
2.93-504.70.03135420.70285.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.424 / Cor.coef. Fo:Fc: 0.519
Highest resolutionLowest resolution
Rotation3 Å29.26 Å
Translation3 Å29.26 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A13

2a13


Resolution: 1.358→47.836 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.526 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1864 4.931 %RANDOM
Rwork0.17 ---
obs0.171 37799 97.155 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 67.43 Å2 / Biso mean: 15.287 Å2 / Biso min: 5.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.657 Å20 Å20 Å2
2---0.694 Å20 Å2
3---0.037 Å2
Refinement stepCycle: LAST / Resolution: 1.358→47.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 47 253 1536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221329
X-RAY DIFFRACTIONr_angle_refined_deg1.3542.0811826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40223.84652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.12915226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.207157
X-RAY DIFFRACTIONr_chiral_restr0.0890.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021010
X-RAY DIFFRACTIONr_nbd_refined0.2050.2555
X-RAY DIFFRACTIONr_nbtor_refined0.2970.2911
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.219
X-RAY DIFFRACTIONr_mcbond_it0.7691.5813
X-RAY DIFFRACTIONr_mcangle_it1.24621288
X-RAY DIFFRACTIONr_scbond_it1.7593597
X-RAY DIFFRACTIONr_scangle_it2.5124.5528
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% reflection obs (%)
1.358-1.3930.2891350.2372582283495.872
1.393-1.4310.2251270.2062602274399.49
1.431-1.4730.2371310.1922564269899.889
1.473-1.5180.2011130.1732483260299.769
1.518-1.5680.2061320.1592387253099.565
1.568-1.6230.171220.1672325245799.593
1.623-1.6840.1811100.1662262238799.372
1.684-1.7530.1991080.1652154228199.167
1.753-1.8310.1871240.162051219998.909
1.831-1.920.172990.161960208798.658
1.92-2.0240.2071020.1581874201098.308
2.024-2.1460.181940.1621778191397.857
2.146-2.2940.1631000.1641649179197.655
2.294-2.4770.212850.171556169396.929
2.477-2.7130.235670.1741425154796.445
2.713-3.0320.179690.1731284142095.282
3.032-3.4990.17590.1581117124894.231
3.499-4.2790.216420.155914107988.601
4.279-6.0280.204350.16464086478.125
6.028-47.8360.423100.2932852364.627
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)
11.7667-0.0689-0.88441.20840.29151.158-0.0677-0.0252-0.03990.01220.015-0.0927-0.07820.1180.05270.04890.0023-0.00750.04070.01560.05685.97039.4478-1.753
24.61084.5944-5.1477.9010.098721.4252-0.29120.1904-1.0416-0.48690.2302-1.43840.2930.97620.0609-0.00260.02950.12690.1126-0.04960.40918.9212-1.3172-4.9326
30.48610.0401-0.28052.23490.29430.8505-0.0077-0.0110.04360.2465-0.0252-0.0057-0.04310.01650.03280.09070.0126-0.0130.0205-0.00990.0491-0.1339.43057.4538
40.87680.3773-0.48691.5109-0.57962.06320.0091-0.07060.04760.1765-0.0213-0.1825-0.10470.18630.01210.0811-0.0113-0.04470.0419-0.00240.064510.52311.84277.5988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 67
2X-RAY DIFFRACTION2A68 - 76
3X-RAY DIFFRACTION3A77 - 109
4X-RAY DIFFRACTION4A110 - 166

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