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- PDB-2qgi: The UDP complex structure of the sixth gene product of the F1-ATP... -

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Basic information

Entry
Database: PDB / ID: 2qgi
TitleThe UDP complex structure of the sixth gene product of the F1-ATPase operon of Rhodobacter blasticus
ComponentsATP synthase subunits region ORF 6
KeywordsTRANSFERASE / MAJASTRIDIN / ATPASE OPERON / GLYCOSYL TRANSFERASE / ROSSMANN FOLD / UDP-COMPLEX
Function / homologySpore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta / : / URIDINE-5'-DIPHOSPHATE / ATP synthase subunits region ORF 6
Function and homology information
Biological speciesRhodobacter blasticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsEnroth, C. / Strid, A.
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: Crystal structure of a protein, structurally related to glycosyltransferases, encoded in the Rhodobacter blasticus atp operon.
Authors: Enroth, C. / Strid, A.
History
DepositionJun 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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: ATP synthase subunits region ORF 6
B: ATP synthase subunits region ORF 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9555
Polymers57,4412
Non-polymers5143
Water12,989721
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-35 kcal/mol
Surface area21120 Å2
MethodPISA
2
A: ATP synthase subunits region ORF 6
B: ATP synthase subunits region ORF 6
hetero molecules

A: ATP synthase subunits region ORF 6
B: ATP synthase subunits region ORF 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,91010
Polymers114,8824
Non-polymers1,0286
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area15230 Å2
ΔGint-88 kcal/mol
Surface area37700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.370, 89.928, 69.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

21B-958-

HOH

31B-985-

HOH

DetailsThe assymmetric unit contains one biological unit, i.e. a dimer.

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Components

#1: Protein ATP synthase subunits region ORF 6 /


Mass: 28720.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter blasticus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P05449
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM sodium citrate (pH6.0) and 75mM magnesium acetate. Mixed 4+4ul with protein sample, hanging drop, vapor diffusion, temperature 298K., VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.043 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.043 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 93646 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.071 / Net I/σ(I): 16.7
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 13554 / Rsym value: 0.388 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.2.17data scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NXV

2nxv


Resolution: 1.65→12.99 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.352 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.184 4687 5 %RANDOM
Rwork0.159 ---
obs0.16 93484 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.201 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.65→12.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 27 721 4788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0214178
X-RAY DIFFRACTIONr_angle_refined_deg2.1041.9415652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49322.314229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83815667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1311546
X-RAY DIFFRACTIONr_chiral_restr0.2740.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023317
X-RAY DIFFRACTIONr_nbd_refined0.2150.21971
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22834
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2557
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.241
X-RAY DIFFRACTIONr_mcbond_it1.5141.52520
X-RAY DIFFRACTIONr_mcangle_it2.1523922
X-RAY DIFFRACTIONr_scbond_it3.48331897
X-RAY DIFFRACTIONr_scangle_it5.3064.51730
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 361 -
Rwork0.228 6404 -
obs-6765 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1864-0.0310.10690.27420.01140.2784-0.0006-0.08130.0192-0.0569-0.0246-0.00880.0138-0.00490.0252-0.0064-0.0046-0.012-0.01250.0047-0.022486.4641.58711.173
20.2782-0.0091-0.15760.2697-0.00330.3260.05140.0682-0.02050.0461-0.0763-0.0151-0.0013-0.01710.0249-0.00530.0043-0.0006-0.01570.0057-0.022786.147-5.083-16.558
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2491 - 248
2X-RAY DIFFRACTION2BB2 - 2491 - 248

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