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- PDB-3oj7: Crystal structure of a histidine triad family protein from entamo... -

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Basic information

Entry
Database: PDB / ID: 3oj7
TitleCrystal structure of a histidine triad family protein from entamoeba histolytica, bound to sulfate
ComponentsPutative histidine triad family protein
KeywordsMETAL BINDING PROTEIN / HYDROLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / 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
Histidine triad nucleotide-binding protein
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSeattle 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 20, 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 1.3Sep 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 / 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)13,1793
Polymers13,0171
Non-polymers1612
Water1,76598
1
A: Putative histidine triad family protein
hetero molecules

A: Putative histidine triad family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3576
Polymers26,0342
Non-polymers3234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area4360 Å2
ΔGint-59 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.890, 61.030, 67.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-167-

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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.09 Å3/Da / Density % sol: 41.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: INTERNAL TRACKING 216243A1. JCSG SCREEN CONDITION A1: 50% PEG400, 0.1 M ACETATE BUFFER PH 4.5, 200 MM LI2SO4, ENHIA.01296.A.A1 PS00632 AT 83.2 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.4→34.37 Å / Num. all: 21814 / Num. obs: 21768 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.03 % / Biso Wilson estimate: 24.26 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 25.27
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 7.12 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1582 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XQU

1xqu
PDB Unreleased entry


Resolution: 1.4→34.37 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.847 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1111 5.1 %RANDOM
Rwork0.162 ---
obs0.163 21706 --
all-21814 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.77 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms856 0 6 98 960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022905
X-RAY DIFFRACTIONr_bond_other_d0.0010.02601
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9641234
X-RAY DIFFRACTIONr_angle_other_deg0.97731495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47625.89739
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72715163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.917151
X-RAY DIFFRACTIONr_chiral_restr0.1050.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021993
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02163
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.991.5555
X-RAY DIFFRACTIONr_mcbond_other0.2791.5223
X-RAY DIFFRACTIONr_mcangle_it1.72908
X-RAY DIFFRACTIONr_scbond_it2.6663350
X-RAY DIFFRACTIONr_scangle_it4.3134.5322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 95 -
Rwork0.247 1479 -
obs--99.75 %
Refinement TLS params.Method: refined / Origin x: 17.8562 Å / Origin y: 23.5031 Å / Origin z: 27.9014 Å
111213212223313233
T0.0336 Å2-0.0137 Å20.022 Å2-0.0161 Å2-0.0146 Å2--0.0262 Å2
L1.2023 °20.3502 °20.3386 °2-1.4579 °20.0847 °2--1.0041 °2
S-0.132 Å °0.0899 Å °-0.1474 Å °-0.1064 Å °0.0958 Å °-0.0736 Å °0.0437 Å °-0.0003 Å °0.0362 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION1A1 - 114

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