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- PDB-1mwq: Structure of HI0828, a Hypothetical Protein from Haemophilus infl... -

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Basic information

Entry
Database: PDB / ID: 1mwq
TitleStructure of HI0828, a Hypothetical Protein from Haemophilus influenzae with a Putative Active-Site Phosphohistidine
ComponentsHYPOTHETICAL PROTEIN HI0828
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HI0828 / YCII_HAEIN / hypothetical protein / Structure 2 Function Project / S2F
Function / homology
Function and homology information


: / YCII-related / YCII-related domain / Dimeric alpha+beta barrel / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / DI(HYDROXYETHYL)ETHER / Uncharacterized protein HI_0828
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.99 Å
AuthorsWillis, M.A. / Krajewski, W. / Chalamasetty, V.R. / Reddy, P. / Howard, A. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2005
Title: Structure of YciI from Haemophilus influenzae (HI0828) reveals a ferredoxin-like alpha/beta-fold with a histidine/aspartate centered catalytic site
Authors: Willis, M.A. / Song, F. / Zhuang, Z. / Krajewski, W. / Chalamasetty, V.R. / Reddy, P. / Howard, A. / Dunaway-Mariano, D. / Herzberg, O.
History
DepositionSep 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _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 HI0828
B: HYPOTHETICAL PROTEIN HI0828
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,56715
Polymers22,6112
Non-polymers95613
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-187 kcal/mol
Surface area10030 Å2
MethodPISA
2
A: HYPOTHETICAL PROTEIN HI0828
hetero molecules

B: HYPOTHETICAL PROTEIN HI0828
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,56715
Polymers22,6112
Non-polymers95613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area2140 Å2
ΔGint-197 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.476, 63.317, 75.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDynamic Light Scattering (DLS) indicates the protein is a dimer in solution. There is one dimer in the asymmetric unit.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HYPOTHETICAL PROTEIN HI0828


Mass: 11305.550 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P44887

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Non-polymers , 6 types, 342 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG4000, sodium cacodylate, sodium chloride, zinc acetate, dioxane, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
216 %PEG40001reservoir
30.1 Msodium cacodylate1reservoirpH5.5
420 mMacetate1reservoir
52 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9793, 0.9795, 0.9664, 0.9832
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 23, 2001
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
30.96641
40.98321
ReflectionResolution: 0.99→19.45 Å / Num. all: 206507 / Num. obs: 206417 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 4.76 % / Rsym value: 0.063 / Net I/σ(I): 16.7
Reflection shellResolution: 0.99→1 Å / Redundancy: 0.87 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3599 / Rsym value: 0.3486 / % possible all: 55.7
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 1042859 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Lowest resolution: 1.1 Å / % possible obs: 83.4 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
XPREPdata reduction
SOLVEphasing
RESOLVEmodel building
CNSrefinement
SHELXmodel building
DENZOdata reduction
RESOLVEphasing
CNSphasing
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 0.99→15 Å / Num. parameters: 18707 / Num. restraintsaints: 23309 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1319 5403 5 %RANDOM
Rwork0.1078 ---
all0.1087 107935 --
obs0.1087 107935 95 %-
Refine analyzeNum. disordered residues: 25 / Occupancy sum hydrogen: 1497 / Occupancy sum non hydrogen: 1916.09
Refinement stepCycle: LAST / Resolution: 0.99→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 38 329 1946
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0269
X-RAY DIFFRACTIONs_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.11
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.036
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.107
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.132 / Rfactor Rwork: 0.109
Solvent computation
*PLUS
Displacement parameters
*PLUS

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