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- PDB-1pzx: Hypothetical protein APC36103 from Bacillus stearothermophilus: a... -

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Basic information

Entry
Database: PDB / ID: 1pzx
TitleHypothetical protein APC36103 from Bacillus stearothermophilus: a lipid binding protein
ComponentsHypothetical protein APC36103
KeywordsLIPID BINDING PROTEIN / Structural genomics / Two domains containing mixed alpha/beta structures / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DegV, N-terminal domain, peripheral subdomain / Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Dihydroxyacetone kinase; domain 1 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / : / Rubrerythrin, domain 2 ...DegV, N-terminal domain, peripheral subdomain / Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Dihydroxyacetone kinase; domain 1 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / : / Rubrerythrin, domain 2 / Single Sheet / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Lipid binding protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, R. / Osipiuk, J. / Zhou, M. / Alkire, R. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Lipid binding protein APC36103 from Bacillus Stearothermophilus
Authors: Zhang, R. / Osipiuk, J. / Zhou, M. / Alkire, R. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionJul 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE SEQUENCE OF THE PROTEIN HAS NOT YET BEEN DEPOSITED IN ANY REFERENCE SEQUENCE DATABASE. ...SEQUENCE THE SEQUENCE OF THE PROTEIN HAS NOT YET BEEN DEPOSITED IN ANY REFERENCE SEQUENCE DATABASE. RESIDUES ASN -1 AND ALA 0 ARE HIS TAG RESIDUES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein APC36103
B: Hypothetical protein APC36103
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3134
Polymers64,8012
Non-polymers5132
Water6,251347
1
A: Hypothetical protein APC36103
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6572
Polymers32,4001
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein APC36103
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6572
Polymers32,4001
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.980, 187.390, 53.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hypothetical protein APC36103


Mass: 32400.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: RBSTP0788 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P83812
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9783 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 23, 2003 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 45723 / Num. obs: 44031 / % possible obs: 96.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 9.63 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 26.45
Reflection shellResolution: 2→2.07 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3.15 / Num. unique all: 4180 / % possible all: 92.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→34.54 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 437806.18 / Data cutoff high rms absF: 437806.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Freidel pairs were used in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3840 4.9 %RANDOM
Rwork0.197 ---
obs0.197 78901 91.3 %-
all-86419 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.932 Å2 / ksol: 0.383831 e/Å3
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å20 Å2
2--4.69 Å20 Å2
3----3.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4467 0 36 347 4850
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 567 4.8 %
Rwork0.293 11296 -
obs--82.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4PLM_XPLOR.PARAM

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