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- PDB-3ia8: The structure of the C-terminal heme nitrobindin domain of THAP d... -

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Basic information

Entry
Database: PDB / ID: 3ia8
TitleThe structure of the C-terminal heme nitrobindin domain of THAP domain-containing protein 4 from Homo sapiens
ComponentsTHAP domain-containing protein 4
KeywordsMETAL BINDING PROTEIN / beta barrel / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG / Heme / THAP domain / THAP4 / DNA-binding / Metal-binding / Phosphoprotein / Zinc-finger
Function / homology
Function and homology information


peroxynitrite isomerase activity / Isomerases; Other isomerases / nitrate metabolic process / tyrosine metabolic process / nitric oxide binding / heme binding / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
THAP / THAP-type zinc finger superfamily / Zinc finger domain in CG10631, C. elegans LIN-15B and human P52rIPK. / THAP-type zinc finger / THAP domain / Zinc finger THAP-type profile / THAP4-like, heme-binding beta-barrel domain / Nitrobindin family / THAP4-like, heme-binding beta-barrel domain / Calycin beta-barrel core domain ...THAP / THAP-type zinc finger superfamily / Zinc finger domain in CG10631, C. elegans LIN-15B and human P52rIPK. / THAP-type zinc finger / THAP domain / Zinc finger THAP-type profile / 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 THAP4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.792 Å
AuthorsBianchetti, C.M. / Bingman, C.A. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2011
Title: Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens.
Authors: Bianchetti, C.M. / Bingman, C.A. / Phillips, G.N.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_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_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.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_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: THAP domain-containing protein 4
B: THAP domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5764
Polymers37,3432
Non-polymers1,2332
Water4,900272
1
A: THAP domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2882
Polymers18,6711
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: THAP domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2882
Polymers18,6711
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-62 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.933, 74.694, 103.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein THAP domain-containing protein 4


Mass: 18671.322 Da / Num. of mol.: 2 / Fragment: sequence database residues 415-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THAP4, CGI-36, PP238 / Plasmid: PVP68K / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q8WY91
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.16 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein Solution (10 mg/ml MSE protein, 0.05 M NaCl, 0.0003 M TCEP, 0.005 M HEPES pH 5) mixed in a 1:1 ratio with the Well Solution (55% Polypropylene glycol 400, 0.1 M Triethanolamine pH 7. ...Details: Protein Solution (10 mg/ml MSE protein, 0.05 M NaCl, 0.0003 M TCEP, 0.005 M HEPES pH 5) mixed in a 1:1 ratio with the Well Solution (55% Polypropylene glycol 400, 0.1 M Triethanolamine pH 7.5). Cryoprotected with 55% Polypropylene glycol 400, 0.1 M Triethanolamine pH 7.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2009 / Details: mirrors and beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionRedundancy: 5.8 % / Av σ(I) over netI: 18.16 / Number: 173743 / Rmerge(I) obs: 0.093 / Χ2: 1.18 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 29918 / % possible obs: 95.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.445099.610.051.5235.6
3.524.4410010.0511.5446
3.083.5210010.0651.2236.1
2.83.0810010.0911.156.1
2.62.810010.1211.196.1
2.442.610010.1391.2136.1
2.322.4410010.1551.156.1
2.222.3210010.1731.1036.1
2.132.2210010.2011.1536.1
2.062.1310010.2361.1035.9
22.0697.710.2641.0785.8
1.94294.410.3021.1135.5
1.891.9487.410.3551.0795.4
1.841.8982.310.4160.9225.1
1.81.8476.210.4570.9354.8
ReflectionResolution: 1.79→50 Å / Num. obs: 29918 / % possible obs: 95.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 19.36 Å2 / Rmerge(I) obs: 0.093 / Χ2: 1.182 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.79-1.844.80.45715570.93576.2
1.84-1.895.10.41616730.92282.3
1.89-1.945.40.35517951.07987.4
1.94-25.50.30219441.11394.4
2-2.065.80.26419731.07897.7
2.06-2.135.90.23620601.103100
2.13-2.226.10.20120741.153100
2.22-2.326.10.17320451.103100
2.32-2.446.10.15520551.15100
2.44-2.66.10.13920811.213100
2.6-2.86.10.12120841.19100
2.8-3.086.10.09120691.15100
3.08-3.526.10.06521211.223100
3.52-4.4460.05121201.544100
4.44-505.60.0522671.52399.6

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_11.7934.4600263353495
ANO_11.7934.460.9630257990
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_17.82-34.4600262169
ISO_15.6-7.8200520182
ISO_14.59-5.600689180
ISO_13.99-4.5900837177
ISO_13.57-3.9900954182
ISO_13.26-3.57001056181
ISO_13.02-3.26001168183
ISO_12.83-3.02001260183
ISO_12.67-2.83001335180
ISO_12.53-2.67001431189
ISO_12.41-2.53001504181
ISO_12.31-2.41001552187
ISO_12.22-2.31001657176
ISO_12.14-2.22001715181
ISO_12.07-2.14001771187
ISO_12-2.07001812174
ISO_11.94-2001808175
ISO_11.89-1.94001763159
ISO_11.84-1.89001677140
ISO_11.79-1.84001564129
ANO_17.82-34.462.55802620
ANO_15.6-7.822.95805200
ANO_14.59-5.62.18306890
ANO_13.99-4.592.00408370
ANO_13.57-3.992.05809540
ANO_13.26-3.571.795010560
ANO_13.02-3.261.64011680
ANO_12.83-3.021.352012600
ANO_12.67-2.831.253013350
ANO_12.53-2.671.062014310
ANO_12.41-2.530.917015040
ANO_12.31-2.410.791015520
ANO_12.22-2.310.659016570
ANO_12.14-2.220.54017140
ANO_12.07-2.140.501017650
ANO_12-2.070.437017910
ANO_11.94-20.38017530
ANO_11.89-1.940.362016750
ANO_11.84-1.890.348015380
ANO_11.79-1.840.321013380
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-0.48633.12475.79SE23.071.26
22.3117.79949.803SE23.11.26
39.36564.36452.514SE20.191.16
48.39163.87611.567SE25.91.2
56.92365.00124.109SE28.191.18
62.30239.91172.979SE29.771.15
73.00340.0294.511SE29.981.16
80.82221.24232.489SE29.571.17
99.36413.33926.409SE34.311.14
108.02363.66365.257SE21.580.96
117.27918.8935.541SE27.620.96
124.8263.065101.723SE31.371.04
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 29829
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.37-10067.40.796512
5.81-7.3760.10.868504
4.99-5.8162.20.882569
4.44-4.9957.90.91629
4.04-4.4462.20.901705
3.73-4.0457.90.899740
3.48-3.7360.20.892817
3.28-3.48650.874852
3.1-3.2864.10.851908
2.96-3.166.80.847947
2.83-2.9666.60.847999
2.72-2.8364.80.8511023
2.62-2.7265.70.8491084
2.53-2.6268.70.8281099
2.44-2.5366.60.8291144
2.37-2.4467.90.8531182
2.3-2.3769.30.8381211
2.24-2.369.30.8451235
2.18-2.2470.90.8631275
2.13-2.1871.90.8591316
2.08-2.1374.20.861327
2.03-2.0876.90.8661373
1.99-2.0378.30.8731344
1.95-1.9977.40.8661366
1.91-1.9578.10.8591322
1.88-1.9176.90.8361280
1.84-1.8878.70.7991232
1.79-1.84810.761834

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM6.1phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.792→35.113 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.14 / σ(F): 1.34 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 1510 5.06 %
Rwork0.165 --
obs0.167 29830 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.54 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 73.45 Å2 / Biso mean: 24.305 Å2 / Biso min: 11.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.125 Å2-0 Å2-0 Å2
2---3.259 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.792→35.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 86 272 2926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092822
X-RAY DIFFRACTIONf_angle_d1.4493883
X-RAY DIFFRACTIONf_chiral_restr0.09412
X-RAY DIFFRACTIONf_plane_restr0.007496
X-RAY DIFFRACTIONf_dihedral_angle_d16.3371049
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.792-1.850.248870.1922017210476
1.85-1.9160.2341230.1882259238285
1.916-1.9930.2031180.1742490260894
1.993-2.0840.2081460.1722609275599
2.084-2.1940.2361530.16626482801100
2.194-2.3310.2191300.16926652795100
2.331-2.5110.231420.1826542796100
2.511-2.7640.2221500.18326942844100
2.764-3.1630.1991470.17226852832100
3.163-3.9850.1631430.14427482891100
3.985-35.1190.1811710.1528513022100

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