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- PDB-3c9q: Crystal structure of the uncharacterized human protein C8orf32 wi... -

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Basic information

Entry
Database: PDB / ID: 3c9q
TitleCrystal structure of the uncharacterized human protein C8orf32 with bound peptide
Components
  • Synthetic peptide
  • Uncharacterized protein C8orf32
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Medically relevant / putative involvement in human inherited ataxias and disorders of Purkinje cell degeneration / candidate gene important in the pathogenesis of T-cell prolymphocytic leukemia / gene associated with CRE-pathway activation / Protein Structure Initiative / PSI-2 / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


protein N-terminal glutamine amidohydrolase / protein-N-terminal glutamine amidohydrolase activity / protein-N-terminal asparagine amidohydrolase activity / protein modification process / nucleus / cytosol
Similarity search - Function
Protein N-terminal glutamine amidohydrolase, alpha beta roll / Protein N-terminal glutamine amidohydrolase, alpha beta roll / Protein N-terminal glutamine amidohydrolase, alpha beta roll superfamily / Protein N-terminal glutamine amidohydrolase / N-terminal glutamine amidase / C8orf32 fold / Roll / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / Protein N-terminal glutamine amidohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsBitto, E. / Bingman, C.A. / McCoy, J.G. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: Crystal structure of the uncharacterized human protein C8orf32 with bound peptide.
Authors: Bitto, E. / Bingman, C.A. / McCoy, J.G. / Wesenberg, G.E. / Phillips Jr., G.N.
History
DepositionFeb 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 16, 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_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_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: Uncharacterized protein C8orf32
L: Synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,85013
Polymers23,9992
Non-polymers85111
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.322, 64.039, 113.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHE BIOLOGICAL UNIT IS THE MONOMERIC COMPLEX OF THE PROTEIN C8ORF32 (CHAIN A) WITH BOUND PEPTIDE (CHAIN L)

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AL

#1: Protein Uncharacterized protein C8orf32


Mass: 23721.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C8orf32 / Plasmid: PVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q96HA8
#2: Protein/peptide Synthetic peptide


Mass: 277.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide

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Non-polymers , 4 types, 283 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 291 K
Details: Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.003 M Sodium azide, 0.0003 M TCEP, Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (1% Ethylene glycol, 1.8 ...Details: Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.003 M Sodium azide, 0.0003 M TCEP, Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (1% Ethylene glycol, 1.8 M Ammonium sulfate, 0.10 M MES pH 6.0). Cryoprotected in four stages with well solution using 0 to 25 % ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.498→32.857 Å / Num. obs: 40943 / % possible obs: 99.5 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 12.075
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.498-1.536.90.5432.52625660.97495.9
1.53-1.578.10.47426500.98897.7
1.57-1.629.50.45526740.9999.2
1.62-1.66110.43326891100
1.66-1.7212.30.38227251.108100
1.72-1.78130.33626871.122100
1.78-1.8513.50.27727061.172100
1.85-1.9313.60.21527221.238100
1.93-2.0413.60.17227331.26100
2.04-2.1613.70.13527331.277100
2.16-2.3313.70.11827401.334100
2.33-2.5613.80.10927601.355100
2.56-2.9413.50.08627691.32100
2.94-3.713.30.06328171.22100
3.7-32.85712.60.05829721.2399.5

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Phasing

PhasingMethod: SAD
Phasing MAD set

R cullis centric: 0 / Highest resolution: 1.5 Å / Lowest resolution: 32.86 Å / Power centric: 0

IDR cullis acentricPower acentricReflection acentricReflection centric
ISO_100362384556
ANO_10.6451.771359780
Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

IDResolution (Å)R cullis acentricPower acentricReflection acentricReflection centric
ISO_16.58-32.8600345217
ISO_14.7-6.5800687230
ISO_13.85-4.700909223
ISO_13.34-3.85001117234
ISO_12.99-3.34001274229
ISO_12.73-2.99001410231
ISO_12.53-2.73001534226
ISO_12.37-2.53001652229
ISO_12.23-2.37001792232
ISO_12.12-2.23001881235
ISO_12.02-2.12001981216
ISO_11.94-2.02002093238
ISO_11.86-1.94002187236
ISO_11.79-1.86002258226
ISO_11.73-1.79002333222
ISO_11.68-1.73002439242
ISO_11.63-1.68002515231
ISO_11.58-1.63002599223
ISO_11.54-1.58002606230
ISO_11.5-1.54002626206
ANO_16.58-32.860.3933.3363450
ANO_14.7-6.580.43.2816870
ANO_13.85-4.70.5222.5289070
ANO_13.34-3.850.4642.89911170
ANO_12.99-3.340.4263.12412720
ANO_12.73-2.990.43.31514080
ANO_12.53-2.730.413.24415340
ANO_12.37-2.530.4273.07516520
ANO_12.23-2.370.4512.84617920
ANO_12.12-2.230.4962.45318810
ANO_12.02-2.120.5442.24719810
ANO_11.94-2.020.591.95120930
ANO_11.86-1.940.6491.7521870
ANO_11.79-1.860.7241.46722580
ANO_11.73-1.790.7581.31323330
ANO_11.68-1.730.8221.15124390
ANO_11.63-1.680.8540.97525110
ANO_11.58-1.630.8880.86125650
ANO_11.54-1.580.9180.82525240
ANO_11.5-1.540.9380.71824920
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
13.97458.56267.447SE11.271.13
29.05423.53791.296SE121.06
35.47228.398106.564SE11.20.91
43.39863.04683.004SE23.190.68
Phasing dmMethod: Solvent flattening and histogram matching / Reflection: 40794
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.84-10063.80.693503
5.24-6.8460.50.897581
4.4-5.2453.50.928705
3.87-4.454.30.936796
3.5-3.8753.70.933884
3.21-3.554.40.923968
2.99-3.2156.70.9131050
2.8-2.99500.9231091
2.65-2.853.40.9221157
2.52-2.6553.20.9141242
2.41-2.5253.40.9181275
2.31-2.4153.40.9241347
2.22-2.3154.30.9141390
2.14-2.2252.90.9221405
2.07-2.1453.40.9161518
2.01-2.0755.60.9161533
1.95-2.0154.70.9071579
1.89-1.9557.30.911612
1.85-1.8956.70.9071682
1.8-1.8560.70.8931687
1.76-1.860.80.8941780
1.72-1.7663.50.8881749
1.68-1.7263.70.8911838
1.65-1.68680.8861839
1.61-1.6567.40.8671916
1.58-1.61690.8691914
1.55-1.58710.8491932
1.53-1.5574.50.8361961
1.5-1.5375.40.7641860

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
SHELXL-97phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→32.857 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.989 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18 2049 5.023 %RANDOM
Rwork0.161 ---
obs0.162 40794 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.013 Å20 Å20 Å2
2--0.122 Å20 Å2
3----0.135 Å2
Refinement stepCycle: LAST / Resolution: 1.5→32.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 49 272 1927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221741
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.9622370
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.49423.8184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12815267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.371159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021351
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2780
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21168
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7931048
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6451671
X-RAY DIFFRACTIONr_scbond_it4.0518800
X-RAY DIFFRACTIONr_scangle_it5.68912696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 144 -
Rwork0.24 2695 -
obs--95.49 %
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)
120.57256.54421.76062.55582.1755.6526-0.02340.34350.3461-0.09830.14480.1978-0.6986-0.0753-0.1214-0.02120.02730.0094-0.13510.006-0.073617.286830.562212.1676
21.65481.2053-0.10252.55360.19861.34430.006-0.00140.0814-0.10930.010.0269-0.1554-0.0992-0.0161-0.11980.01030.0002-0.10430.0037-0.134719.15920.02617.3989
32.0253-0.1079-0.62462.42830.08822.7045-0.0327-0.0773-0.0859-0.0939-0.0374-0.15770.11210.07630.0701-0.15840.0148-0.0327-0.1155-0.0165-0.153523.037315.794419.5667
42.43540.1269-1.05641.2684-0.7621.93690.0913-0.1860.20770.1494-0.10280.1259-0.1213-0.13950.0115-0.11-0.0047-0.015-0.0838-0.0127-0.11415.535418.136321.3008
50.225-0.2146-0.25733.5058-1.81821.5842-0.001-0.11550.02340.3246-0.0198-0.0365-0.1690.0060.0208-0.1145-0.0165-0.0036-0.0917-0.0035-0.112917.791618.717326.8157
60.1766-0.08190.32321.39540.47143.54390.0097-0.049-0.1253-0.0468-0.0127-0.06250.04550.05970.003-0.13830.02940.0034-0.12870.0027-0.105226.056311.15211.2026
726.7925-0.851-5.970222.0417-4.451812.8940.2108-0.3914-2.819-0.1007-0.32730.20971.42310.00140.11650.0754-0.0739-0.0587-0.00870.02120.15639.1638-0.67585.8466
85.5782-0.50290.8470.7653-0.06821.06580.00640.1692-0.3683-0.0873-0.0269-0.03470.14520.11420.0205-0.0906-0.00750.0067-0.0558-0.0281-0.108420.57518.9742.0155
91.23190.31630.06990.73791.7764.71050.0413-0.1678-0.10340.1742-0.0616-0.10260.24660.32620.0203-0.08940.0088-0.0138-0.04070.0308-0.06229.712911.661222.065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 1812 - 18
2X-RAY DIFFRACTION2AA19 - 4219 - 42
3X-RAY DIFFRACTION3AA43 - 6543 - 65
4X-RAY DIFFRACTION4AA66 - 9266 - 92
5X-RAY DIFFRACTION5AA93 - 12893 - 128
6X-RAY DIFFRACTION6AA129 - 149129 - 149
7X-RAY DIFFRACTION7AA150 - 157150 - 157
8X-RAY DIFFRACTION8AA158 - 173158 - 173
9X-RAY DIFFRACTION9AA174 - 202174 - 202

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