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- PDB-2o2z: Crystal structure of a protein member of the upf0052 family (bh35... -

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Basic information

Entry
Database: PDB / ID: 2o2z
TitleCrystal structure of a protein member of the upf0052 family (bh3568) from bacillus halodurans at 2.60 A resolution
Componentshypothetical protein
KeywordsNAD-BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


LPPG:FO 2-phospho-L-lactate transferase activity / regulation of cell shape / cytoplasm
Similarity search - Function
Gluconeogenesis factor / CofD-like domains / 2-phospho-L-lactate transferase CofD / CofD-like domain superfamily / 2-phospho-L-lactate transferase CofD / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Gluconeogenesis factor
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_244435.1) from Bacillus halodurans at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DNA SEQUENCING INDICATES THAT RESIDUE 7 IS ISOLEUCINE (NOT VALINE) IN THE CLONED CONSTRUCT. THE SEQUENCING RESULTS ARE CONSISTENT WITH THE ELECTRON DENSITY AND MASS SPECTROMETRY RESULTS FOR THE EXPRESSED PROTEIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
C: hypothetical protein
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,75916
Polymers139,3374
Non-polymers3,42212
Water5,044280
1
A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3798
Polymers69,6682
Non-polymers1,7116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-105 kcal/mol
Surface area24770 Å2
MethodPISA
2
C: hypothetical protein
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3798
Polymers69,6682
Non-polymers1,7116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-106 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.430, 143.640, 233.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSVALVAL2AA4 - 1185 - 119
21LYSLYSVALVAL2BB4 - 1185 - 119
31LYSLYSVALVAL2CC4 - 1185 - 119
41LYSLYSVALVAL2DD4 - 1185 - 119
52ARGARGARGARG6AA119120
62ARGARGARGARG6BB119120
72ARGARGARGARG6CC119120
82ARGARGARGARG6DD119120
93GLYGLYILEILE2AA120 - 310121 - 311
103GLYGLYILEILE2BB120 - 310121 - 311
113GLYGLYILEILE2CC120 - 310121 - 311
123GLYGLYILEILE2DD120 - 310121 - 311
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
hypothetical protein


Mass: 34834.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: NP_244435.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K706
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.5
Details: 40.0% polyethylene glycol 400, 0.2M lithium sulfate, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2006
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.6→29.437 Å / Num. obs: 54381 / % possible obs: 99.6 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.41
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obs% possible all
2.6-2.690.4012.93399797.5
2.69-2.80.3393.740153100
2.8-2.930.2734.740574100
2.93-3.080.1966.938502100
3.08-3.270.1449.339080100
3.27-3.520.09513.73927799.9
3.52-3.880.0620.840256100
3.88-4.430.04626.63886199.9
4.43-5.570.04329.73920699.9
5.57-29.40.029353903298.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.437 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.913 / SU B: 16.706 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.425 / ESU R Free: 0.255
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ONE NAD IS ASSOCIATED WITH EACH MONOMER. NAD IS ASSIGNED BASED ON ELECTRON DENSITY. THE ASSIGNMENT IS TENTATIVE DUE TO POOR DENSITY ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ONE NAD IS ASSOCIATED WITH EACH MONOMER. NAD IS ASSIGNED BASED ON ELECTRON DENSITY. THE ASSIGNMENT IS TENTATIVE DUE TO POOR DENSITY AND LIMITED RESOLUTION, ONLY PYROPHOSPHATE AND RIBOSE DENSITY ARE DEFINITIVE. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPOR DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2764 5.1 %RANDOM
Rwork0.188 ---
obs0.19 54312 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.271 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2--0.2 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9095 0 216 280 9591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229442
X-RAY DIFFRACTIONr_bond_other_d0.0020.026217
X-RAY DIFFRACTIONr_angle_refined_deg1.52.01812822
X-RAY DIFFRACTIONr_angle_other_deg0.92315382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49251226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5624.936312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.916151618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8141542
X-RAY DIFFRACTIONr_chiral_restr0.0720.21559
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210234
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021610
X-RAY DIFFRACTIONr_nbd_refined0.2160.21874
X-RAY DIFFRACTIONr_nbd_other0.1880.26251
X-RAY DIFFRACTIONr_nbtor_refined0.1750.24557
X-RAY DIFFRACTIONr_nbtor_other0.0860.25055
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2340
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0810.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.24
X-RAY DIFFRACTIONr_mcbond_it1.56636313
X-RAY DIFFRACTIONr_mcbond_other0.23832543
X-RAY DIFFRACTIONr_mcangle_it2.659827
X-RAY DIFFRACTIONr_scbond_it4.89983518
X-RAY DIFFRACTIONr_scangle_it6.797112995
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1766TIGHT POSITIONAL0.040.05
2B1766TIGHT POSITIONAL0.040.05
3C1766TIGHT POSITIONAL0.040.05
4D1766TIGHT POSITIONAL0.040.05
1A1869MEDIUM POSITIONAL0.340.5
2B1869MEDIUM POSITIONAL0.30.5
3C1869MEDIUM POSITIONAL0.280.5
4D1869MEDIUM POSITIONAL0.290.5
1A6LOOSE POSITIONAL0.135
2B6LOOSE POSITIONAL0.335
3C6LOOSE POSITIONAL0.385
4D6LOOSE POSITIONAL0.625
1A1766TIGHT THERMAL0.110.5
2B1766TIGHT THERMAL0.110.5
3C1766TIGHT THERMAL0.090.5
4D1766TIGHT THERMAL0.10.5
1A1869MEDIUM THERMAL0.882
2B1869MEDIUM THERMAL0.782
3C1869MEDIUM THERMAL0.72
4D1869MEDIUM THERMAL0.732
1A6LOOSE THERMAL0.9710
2B6LOOSE THERMAL1.4210
3C6LOOSE THERMAL1.2410
4D6LOOSE THERMAL1.2910
LS refinement shellResolution: 2.599→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 205 -
Rwork0.235 3654 -
obs-3859 97.8 %

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