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- PDB-1y23: Crystal structure of a member of HIT family of proteins from baci... -

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Basic information

Entry
Database: PDB / ID: 1y23
TitleCrystal structure of a member of HIT family of proteins from bacillus subtilis
ComponentsHistidine triad protein
KeywordsCELL CYCLE / HIT protein / PKCI-1 / cell-cycle regulation / histidine triad / NYSGXRC / Structural Genomics / Protein Structure Initiative / T2097 / New York SGX Research Center for Structural Genomics / PSI
Function / homology
Function and homology information


nucleotide metabolic process / catalytic activity
Similarity search - Function
HIT-like / HINT family / 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 / HINT family / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å
AuthorsRajashankar, K.R. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a member of HIT family of proteins from bacillus subtilis
Authors: Rajashankar, K.R. / Lima, C.D.
History
DepositionNov 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_special_symmetry
Revision 1.4Feb 3, 2021Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_asym_id / _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_asym_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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine triad protein
B: Histidine triad protein
C: Histidine triad protein
D: Histidine triad protein
E: Histidine triad protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,96411
Polymers81,6125
Non-polymers3516
Water5,170287
1
A: Histidine triad protein
B: Histidine triad protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8005
Polymers32,6452
Non-polymers1553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-54 kcal/mol
Surface area12670 Å2
MethodPISA
2
C: Histidine triad protein
D: Histidine triad protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7764
Polymers32,6452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-50 kcal/mol
Surface area12490 Å2
MethodPISA
3
E: Histidine triad protein
hetero molecules

E: Histidine triad protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7764
Polymers32,6452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Unit cell
Length a, b, c (Å)86.444, 86.444, 180.046
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11E-1086-

HOH

DetailsBiological molecule is a dimer. Protomers A and B together form one biological assembly and so do protomers C and D. The partner protomer for molecule E is generated by the crystallographic two fold operation x, -y, -z+2/3

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Components

#1: Protein
Histidine triad protein / HIT


Mass: 16322.483 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yhaE, HIT / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834, DE3 / References: UniProt: O07513
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.38 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 19.5% Peg 4000, 0.5M Ammonium Acetate, 0.1M Sodium Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→19.96 Å / Num. all: 35084 / Num. obs: 35084 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.5 % / Biso Wilson estimate: 18.7 Å2 / Rsym value: 0.086
Reflection shellResolution: 2.3→2.38 Å / Num. unique all: 3452 / Rsym value: 0.363 / % possible all: 99.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1.1refinement
RefinementMethod to determine structure: SIRAS
Starting model: Experimental electron density map from Hg SIRAS density modified phases

Resolution: 2.3→19.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 248233.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1644 5 %RANDOM
Rwork0.213 ---
all0.2131 ---
obs0.2131 33077 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.848 Å2 / ksol: 0.368286 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.35 Å23.27 Å20 Å2
2--4.35 Å20 Å2
3----8.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5561 0 6 287 5854
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.852.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 270 5.3 %
Rwork0.252 4817 -
obs--87.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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