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- PDB-3omf: Crystal structure of a histidine triad family protein from Entamo... -

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Basic information

Entry
Database: PDB / ID: 3omf
TitleCrystal structure of a histidine triad family protein from Entamoeba histolytica, bound to AMP
ComponentsPutative histidine triad family protein
KeywordsMETAL BINDING PROTEIN / SSGCID / putative hydrolase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / sulfur compound metabolic process / hydrolase activity / nucleotide binding / nucleus / cytoplasm
Similarity search - Function
Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Histidine triad nucleotide-binding protein
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / molecular replacement, molecular replacement / molecular replacement / Resolution: 1.8 Å
AuthorsSSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structures of a histidine triad family protein from Entamoeba histolytica bound to sulfate, AMP and GMP.
Authors: Lorimer, D.D. / Choi, R. / Abramov, A. / Nakazawa Hewitt, S. / Gardberg, A.S. / Van Voorhis, W.C. / Staker, B.L. / Myler, P.J. / Edwards, T.E.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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: Putative histidine triad family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4303
Polymers13,0171
Non-polymers4132
Water2,972165
1
A: Putative histidine triad family protein
hetero molecules

A: Putative histidine triad family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8596
Polymers26,0342
Non-polymers8254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5490 Å2
ΔGint-32 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.580, 60.630, 67.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-130-

HOH

21A-274-

HOH

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Components

#1: Protein Putative histidine triad family protein


Mass: 13017.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EHI_093910 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4LYI2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Internal tracking number 217183B6. JCSG screen condition B6: 40% v/v ethanol, 5% w/v PEG 1000, phosphate-citrate buffer pH 4.2, EnhiA.01296.a.A1 PS00632 at 83.2 mg/ml, 10 mM AMP, VAPOR ...Details: Internal tracking number 217183B6. JCSG screen condition B6: 40% v/v ethanol, 5% w/v PEG 1000, phosphate-citrate buffer pH 4.2, EnhiA.01296.a.A1 PS00632 at 83.2 mg/ml, 10 mM AMP, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→34.56 Å / Num. all: 10570 / Num. obs: 9684 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 16.256 Å2 / Rmerge(I) obs: 0.023 / Net I/σ(I): 52.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.853.70.04521.4233862680.3
1.85-1.90.05821.7251559681.1
1.9-1.950.04730.4278561784.6
1.95-2.010.03531.1288562186.7
2.01-2.080.03134.8280861590
2.08-2.150.02937.9285161092
2.15-2.230.03139.8269759592.1
2.23-2.320.03245.2279958293
2.32-2.430.02449.6307055895.2
2.43-2.550.02356.9327655995.9
2.55-2.680.02358.4307651695.7
2.68-2.850.02161.6316649495.9
2.85-3.040.02168.1315946996.5
3.04-3.290.0276.7327144296.9
3.29-3.60.0288.6356541596.7
3.6-4.030.02192.1318737597.9
4.03-4.650.019101.5291933798.5
4.65-5.690.01998.4247128797.6
5.69-8.050.01891.9192823599.6
8.050.01894.799113594.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.56 Å
Translation2.5 Å34.56 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: molecular replacement, molecular replacement
Starting model: 3OJ7

3oj7


Resolution: 1.8→34.56 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.692 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 467 4.8 %RANDOM
Rwork0.146 ---
all0.148 10570 --
obs0.148 9660 91.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.817 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms879 0 24 165 1068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022942
X-RAY DIFFRACTIONr_bond_other_d0.0010.02632
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9951283
X-RAY DIFFRACTIONr_angle_other_deg0.90131570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3325116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72725.89739
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42615172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.708151
X-RAY DIFFRACTIONr_chiral_restr0.0810.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211013
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02170
X-RAY DIFFRACTIONr_mcbond_it0.6391.5562
X-RAY DIFFRACTIONr_mcbond_other0.1651.5226
X-RAY DIFFRACTIONr_mcangle_it1.1972919
X-RAY DIFFRACTIONr_scbond_it1.9223380
X-RAY DIFFRACTIONr_scangle_it3.1854.5361
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 27 -
Rwork0.146 596 -
all-623 -
obs--79.97 %
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)
10.24410.0399-0.03890.4101-0.03680.4565-0.01820.01290.0313-0.01330.01790.0006-0.01860.01560.00030.0027-0.0023-0.00240.0023-0.00040.02368.3936.993-5.82
20.0058-0.00110.00340.00080.00150.0105-0.0030.0067-0.0448-0.00550.00760.0133-0.03120.0246-0.00460.1277-0.0463-0.00260.0802-0.00550.38311.2137.767-12.033
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 113
2X-RAY DIFFRACTION1A1 - 114
3X-RAY DIFFRACTION2A1 - 115

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