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- PDB-3ky8: Crystal structure of Putative riboflavin biosynthesis protein (YP... -

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Basic information

Entry
Database: PDB / ID: 3ky8
TitleCrystal structure of Putative riboflavin biosynthesis protein (YP_001092907.1) from SHEWANELLA SP. PV-4 at 2.12 A resolution
ComponentsPutative riboflavin biosynthesis proteinRiboflavin
KeywordsBIOSYNTHETIC PROTEIN / Putative riboflavin biosynthesis protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process
Similarity search - Function
Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Bifunctional deaminase-reductase domain protein
Similarity search - Component
Biological speciesShewanella loihica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative riboflavin biosynthesis protein (YP_001092907.1) from SHEWANELLA SP. PV-4 at 2.12 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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: Putative riboflavin biosynthesis protein
B: Putative riboflavin biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,74814
Polymers44,9952
Non-polymers75312
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-90 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.679, 72.679, 156.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 176
2114B1 - 176
DetailsCRYSTAL PACKING AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative riboflavin biosynthesis protein / Riboflavin / Bifunctional deaminase-reductase domain protein


Mass: 22497.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica (bacteria) / Strain: ATCC BAA-1088 / PV-4 / Gene: Shew_0776 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3QB00
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 1-178) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5000M (NH4)2SO4, 1.0000M Li2SO4, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97917,0.97870
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 9, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979171
30.97871
ReflectionResolution: 2.12→30.029 Å / Num. obs: 24676 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.549 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.12-2.20.9481.5175884765199.2
2.2-2.280.7692158364140199.3
2.28-2.390.6342.4184134788199.5
2.39-2.510.4653.2168654373199.9
2.51-2.670.3624.1177494589199.7
2.67-2.880.2286.2179264640199.8
2.88-3.160.13110.3171264421199.8
3.16-3.620.06918.3178294595199.9
3.62-4.550.03730.4177134559199.9
4.55-30.0290.02937.9179024615199.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.12→30.029 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 10.193 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.182
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SULFATE (SO4) IONS AND GLYCEROL (GOL) MOLECULES ARE MODELED BASED ON CRYSTALLIZATION CONDITION. 5. UNIDENTIFIED LIGANDS (UNL) HAVE BEEN MODELED IN ELECTRON DENSITY FOUND NEAR THE PUTATIVE ACTIVE SITES.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1256 5.1 %RANDOM
Rwork0.181 ---
obs0.184 24610 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.03 Å2 / Biso mean: 37.954 Å2 / Biso min: 15.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20 Å2
2--1.43 Å20 Å2
3----2.86 Å2
Refinement stepCycle: LAST / Resolution: 2.12→30.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 76 197 3084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222940
X-RAY DIFFRACTIONr_bond_other_d0.0020.021921
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9823994
X-RAY DIFFRACTIONr_angle_other_deg0.96134720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4275367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.49525.312128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.815493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1081510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
X-RAY DIFFRACTIONr_nbd_refined0.250.2473
X-RAY DIFFRACTIONr_nbd_other0.1990.21947
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21408
X-RAY DIFFRACTIONr_nbtor_other0.0880.21581
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2141
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.213
X-RAY DIFFRACTIONr_mcbond_it1.98331877
X-RAY DIFFRACTIONr_mcbond_other0.6753743
X-RAY DIFFRACTIONr_mcangle_it2.86552943
X-RAY DIFFRACTIONr_scbond_it4.91681218
X-RAY DIFFRACTIONr_scangle_it6.566111051
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2202 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.720.5
MEDIUM THERMAL1.32
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 82 -
Rwork0.254 1686 -
all-1768 -
obs--99.49 %
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)
11.3919-0.1582-0.30570.88890.31081.26950.0042-0.1060.02050.05170.0320.02690.0356-0.0884-0.0362-0.04750.0197-0.0167-0.10970.0225-0.095412.31322.377462.6231
20.8282-0.5436-1.01691.42690.63741.25180.00090.02940.0208-0.13710.0159-0.1212-0.06430.1001-0.0168-0.04430.014-0.0029-0.06090.0009-0.070531.019410.83239.7749
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 177
2X-RAY DIFFRACTION2B1 - 177

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