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- PDB-1no5: Structure of HI0073 from Haemophilus influenzae, the nucleotide b... -

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Basic information

Entry
Database: PDB / ID: 1no5
TitleStructure of HI0073 from Haemophilus influenzae, the nucleotide binding domain of the HI0073/HI0074 two protein nucleotidyl transferase.
ComponentsHypothetical protein HI0073
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HI0073 / HI0074 / nucleotidyl transferase / Structure 2 Function Project / S2F
Function / homology
Function and homology information


protein adenylyltransferase / nucleotidyltransferase activity / ATP binding / metal ion binding
Similarity search - Function
: / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable protein adenylyltransferase MntA
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLehmann, C. / Pullalarevu, S. / Galkin, A. / Krajewski, W. / Willis, M.A. / Howard, A. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2005
Title: Structure of HI0073 from Haemophilus influenzae, the nucleotide-binding domain of a two-protein nucleotidyl transferase
Authors: Lehmann, C. / Pullalarevu, S. / Krajewski, W. / Willis, M.A. / Galkin, A. / Howard, A. / Herzberg, O.
History
DepositionJan 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein HI0073
B: Hypothetical protein HI0073
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,22314
Polymers26,3922
Non-polymers83012
Water5,477304
1
A: Hypothetical protein HI0073
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6157
Polymers13,1961
Non-polymers4196
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hypothetical protein HI0073
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6077
Polymers13,1961
Non-polymers4116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Hypothetical protein HI0073
B: Hypothetical protein HI0073
hetero molecules

A: Hypothetical protein HI0073
B: Hypothetical protein HI0073
hetero molecules

A: Hypothetical protein HI0073
B: Hypothetical protein HI0073
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,66842
Polymers79,1776
Non-polymers2,49136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9060 Å2
ΔGint-886 kcal/mol
Surface area32750 Å2
MethodPISA
4
A: Hypothetical protein HI0073
hetero molecules

A: Hypothetical protein HI0073
hetero molecules

A: Hypothetical protein HI0073
hetero molecules

B: Hypothetical protein HI0073
hetero molecules

B: Hypothetical protein HI0073
hetero molecules

B: Hypothetical protein HI0073
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,66842
Polymers79,1776
Non-polymers2,49136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation4_665-x+1,-y+1,z+1/21
crystal symmetry operation5_555y,-x+y,z+1/21
crystal symmetry operation6_655x-y+1,x,z+1/21
Buried area8570 Å2
ΔGint-872 kcal/mol
Surface area33240 Å2
MethodPISA
5
A: Hypothetical protein HI0073
hetero molecules

B: Hypothetical protein HI0073
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,22314
Polymers26,3922
Non-polymers83012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z+1/21
Buried area2180 Å2
ΔGint-281 kcal/mol
Surface area11760 Å2
MethodPISA
6
A: Hypothetical protein HI0073
hetero molecules

B: Hypothetical protein HI0073
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,22314
Polymers26,3922
Non-polymers83012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area2210 Å2
ΔGint-279 kcal/mol
Surface area11730 Å2
MethodPISA
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-205 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.56, 89.56, 61.48
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hypothetical protein HI0073


Mass: 13196.114 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0073 / Plasmid: pHI0073 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P43933

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Non-polymers , 5 types, 316 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.2 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% 2-Propanol, 0.1 M Sodium cacodylate, 0.2 M Zn(acetate)2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMTris-HCl1droppH7.5
21 mMEDTA1drop
315 mg/mlprotein1drop
411 %2-propanol1reservoir
50.1 Msodium cacodylate1reservoirpH6.5
60.2 Mzinc acetate1reservoir

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 13, 2002 / Details: mirror
RadiationMonochromator: Si(111) double crystal system / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→19.79 Å / Num. all: 51005 / Num. obs: 51005 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 32.14
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 5 / Num. unique all: 2558 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 19.8 Å / % possible obs: 0.028 % / Num. measured all: 960910
Reflection shell
*PLUS
Lowest resolution: 1.85 Å / % possible obs: 100 %

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.79 Å / Num. parameters: 7935 / Num. restraintsaints: 6841 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2532 5.2 %RANDOM
Rwork0.2003 ---
all-48448 --
obs-48448 100 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1975
Refinement stepCycle: LAST / Resolution: 1.8→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 25 304 1975
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0274
X-RAY DIFFRACTIONs_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.105
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 19.8 Å / Rfactor obs: 0.201 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.027
X-RAY DIFFRACTIONs_chiral_restr0.05

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