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- PDB-1zke: 1.6 A Crystal Structure of a Protein HP1531 of Unknown Function f... -

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Basic information

Entry
Database: PDB / ID: 1zke
Title1.6 A Crystal Structure of a Protein HP1531 of Unknown Function from Helicobacter pylori
ComponentsHypothetical protein HP1531Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Helicobacter pylori / layer of helix-turn-helix / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyProtein of unknown function DUF2443 / Uncharacterised protein HP_1531 / Protein of unknown function (DUF2443) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / Uncharacterized protein HP_1531
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.6A crystal structure of a hypothetical protein HP1531 from Helicobacter pylori 26695
Authors: Zhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMay 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_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: Hypothetical protein HP1531
B: Hypothetical protein HP1531
C: Hypothetical protein HP1531
D: Hypothetical protein HP1531
E: Hypothetical protein HP1531
F: Hypothetical protein HP1531
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,79810
Polymers56,7006
Non-polymers974
Water13,565753
1
A: Hypothetical protein HP1531
C: Hypothetical protein HP1531
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9243
Polymers18,9002
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-29 kcal/mol
Surface area9510 Å2
MethodPISA
2
B: Hypothetical protein HP1531
F: Hypothetical protein HP1531
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9243
Polymers18,9002
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-18 kcal/mol
Surface area9600 Å2
MethodPISA
3
D: Hypothetical protein HP1531
E: Hypothetical protein HP1531
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9494
Polymers18,9002
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-27 kcal/mol
Surface area9640 Å2
MethodPISA
4
A: Hypothetical protein HP1531
C: Hypothetical protein HP1531
hetero molecules

B: Hypothetical protein HP1531
F: Hypothetical protein HP1531
hetero molecules

D: Hypothetical protein HP1531
E: Hypothetical protein HP1531
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,79810
Polymers56,7006
Non-polymers974
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
crystal symmetry operation3_654-x+1,y+1/2,-z-1/21
Buried area11230 Å2
ΔGint-95 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.156, 73.262, 135.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein existed as dimer. MolA and MolC form the dimer in this deposition.

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Components

#1: Protein
Hypothetical protein HP1531 / Hypothesis


Mass: 9450.053 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: GI:15646139 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P64665
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG3350, 0.1M NH4SO4, 0.1M Bis-Tris., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 75865 / % possible obs: 92.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 16.57 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.48
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.73 / Num. unique all: 14527 / % possible all: 67.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→67.73 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.72 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.101
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23181 3613 5.1 %RANDOM
Rwork0.19819 ---
obs0.19996 67687 93.98 %-
all-72023 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.567 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---0.89 Å20 Å2
3----0.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.081 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.082 Å
Refinement stepCycle: LAST / Resolution: 1.6→67.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3930 0 4 753 4687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223964
X-RAY DIFFRACTIONr_angle_refined_deg1.1992.0085278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1225486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.45526.067178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06715868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1631518
X-RAY DIFFRACTIONr_chiral_restr0.0740.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022820
X-RAY DIFFRACTIONr_nbd_refined0.2010.22035
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22822
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2543
X-RAY DIFFRACTIONr_metal_ion_refined0.2530.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.2174
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.299
X-RAY DIFFRACTIONr_mcbond_it0.7771.52504
X-RAY DIFFRACTIONr_mcangle_it1.32523900
X-RAY DIFFRACTIONr_scbond_it2.77131568
X-RAY DIFFRACTIONr_scangle_it4.2894.51378
LS refinement shellResolution: 1.599→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 208 -
Rwork0.234 3691 -
obs--70.43 %
Refinement TLS params.Method: refined / Origin x: 28.422 Å / Origin y: 31.619 Å / Origin z: -0.173 Å
111213212223313233
T0.1419 Å2-0.006 Å20.0007 Å2-0.025 Å2-0.0002 Å2--0.0328 Å2
L0.0087 °2-0.0055 °20.0305 °2-0.0053 °2-0.0009 °2--0.28 °2
S0.0017 Å °-0.0004 Å °0.005 Å °-0.0031 Å °0.011 Å °0.0114 Å °-0.0435 Å °0.0209 Å °-0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 813 - 83
2X-RAY DIFFRACTION1BB0 - 812 - 83
3X-RAY DIFFRACTION1CC1 - 813 - 83
4X-RAY DIFFRACTION1DD-1 - 811 - 83
5X-RAY DIFFRACTION1EE0 - 812 - 83
6X-RAY DIFFRACTION1FF-1 - 811 - 83

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