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- PDB-1vp8: CRYSTAL STRUCTURE OF an alpha/beta domain of a putative pyruvate ... -

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Basic information

Entry
Database: PDB / ID: 1vp8
TitleCRYSTAL STRUCTURE OF an alpha/beta domain of a putative pyruvate kinase (AF0103) FROM ARCHAEOGLOBUS FULGIDUS DSM 4304 AT 1.30 A RESOLUTION
Componentshypothetical protein AF0103Hypothesis
KeywordsFLAVOPROTEIN / PUTATIVE PYRUVATE KINASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


Protein of unknown function DUF1867 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Unknown ligand / PK_C domain-containing protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_068944.1) from Archaeoglobus fulgidus at 1.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein AF0103
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1543
Polymers22,6981
Non-polymers4562
Water2,792155
1
A: hypothetical protein AF0103
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)138,92618
Polymers136,1886
Non-polymers2,73812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area30710 Å2
ΔGint-162 kcal/mol
Surface area33290 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)109.650, 109.650, 76.451
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein hypothetical protein AF0103 / Hypothesis


Mass: 22697.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: NP_068944.1 / Production host: Escherichia coli (E. coli) / References: UniProt: O30133
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.78 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 50.0% PEG-200, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.3.111.000034
SYNCHROTRONALS 8.3.121.019859,0.979547,0.979667
DetectorType: ADSC / Detector: CCD / Date: Aug 28, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0000341
21.0198591
30.9795471
40.9796671
ReflectionResolution: 1.3→24.9 Å / Num. obs: 66691 / % possible obs: 100 % / Redundancy: 14.4 % / Biso Wilson estimate: 18.46 Å2 / Rsym value: 0.085 / Net I/σ(I): 21.9
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 2 / Num. unique all: 4852 / Rsym value: 0.974 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.3→24.61 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.004 / SU ML: 0.022 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN UNKNOWN LIGAND HAS BEEN MODELED NEAR THE FMN GROUP.
RfactorNum. reflection% reflectionSelection details
Rfree0.16633 3335 5 %RANDOM
Rwork0.15436 ---
obs0.15499 63320 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.017 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.3→24.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 38 155 1634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221563
X-RAY DIFFRACTIONr_bond_other_d0.0020.021529
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9972118
X-RAY DIFFRACTIONr_angle_other_deg0.97333547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5723.28467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88715306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2721516
X-RAY DIFFRACTIONr_chiral_restr0.0990.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021665
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02294
X-RAY DIFFRACTIONr_nbd_refined0.2170.2284
X-RAY DIFFRACTIONr_nbd_other0.1980.21555
X-RAY DIFFRACTIONr_nbtor_other0.0870.2907
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.219
X-RAY DIFFRACTIONr_mcbond_it1.71331022
X-RAY DIFFRACTIONr_mcbond_other0.2953392
X-RAY DIFFRACTIONr_mcangle_it1.80151567
X-RAY DIFFRACTIONr_scbond_it3.5328674
X-RAY DIFFRACTIONr_scangle_it4.81211551
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2780
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 229 4.73 %
Rwork0.278 4613 -
obs--99.81 %
Refinement TLS params.Method: refined / Origin x: 41.035 Å / Origin y: 8.271 Å / Origin z: 23.207 Å
111213212223313233
T-0.0281 Å2-0.0255 Å2-0.0013 Å2--0.0722 Å20.0065 Å2---0.0577 Å2
L0.4682 °2-0.0485 °20.0503 °2-0.6234 °2-0.1275 °2--0.5325 °2
S0.0272 Å °-0.0231 Å °-0.1238 Å °0.0277 Å °0.01 Å °0.1057 Å °0.1527 Å °-0.0981 Å °-0.0371 Å °
Refinement TLS groupSelection: ALL

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