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- PDB-4ffj: The crystal structure of spDHBPs from S.pneumoniae -

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Basic information

Entry
Database: PDB / ID: 4ffj
TitleThe crystal structure of spDHBPs from S.pneumoniae
ComponentsRiboflavin biosynthesis protein ribBARiboflavin
KeywordsLYASE / Barrel structure
Function / homology
Function and homology information


GTP cyclohydrolase II / GTP cyclohydrolase II activity / 3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / manganese ion binding / GTP binding / magnesium ion binding / zinc ion binding
Similarity search - Function
Riboflavin biosynthesis protein RibBA / GTP cyclohydrolase II, RibA / GTP cyclohydrolase II / GTP cyclohydrolase II superfamily / GTP cyclohydrolase II / DHBP synthase / 3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB / 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily ...Riboflavin biosynthesis protein RibBA / GTP cyclohydrolase II, RibA / GTP cyclohydrolase II / GTP cyclohydrolase II superfamily / GTP cyclohydrolase II / DHBP synthase / 3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB / 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Riboflavin biosynthesis protein RibBA / Riboflavin biosynthesis protein RibBA
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, D.
CitationJournal: To be Published
Title: The crystal structure of SpDHBPs from S. pneumoniae
Authors: Wang, D.
History
DepositionJun 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Riboflavin biosynthesis protein ribBA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3989
Polymers23,6491
Non-polymers7498
Water2,180121
1
A: Riboflavin biosynthesis protein ribBA
hetero molecules

A: Riboflavin biosynthesis protein ribBA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,79618
Polymers47,2982
Non-polymers1,49716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5600 Å2
ΔGint-89 kcal/mol
Surface area16340 Å2
MethodPISA
2
A: Riboflavin biosynthesis protein ribBA
hetero molecules

A: Riboflavin biosynthesis protein ribBA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,79618
Polymers47,2982
Non-polymers1,49716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4080 Å2
ΔGint-68 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.008, 78.008, 87.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-449-

HOH

21A-494-

HOH

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Components

#1: Protein Riboflavin biosynthesis protein ribBA / Riboflavin


Mass: 23649.227 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ribAB, ribBA, SP_0176 / References: UniProt: Q97SY7, UniProt: A0A0H2UN41*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


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


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.02
Details: 2M NH4)2SO4,pH7.02 BisTris 0.1M, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 181062 / Num. obs: 20622 / % possible obs: 89.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.8 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.066 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.4-2.638.80.17623540.167192
2.63-2.949.10.09921650.093192.6
2.94-3.399.40.05519380.052193.2
3.39-4.169.40.04216700.039194.1
4.16-5.889.30.02813130.027194.1
5.88-508.90.0237390.022189.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MERLOTphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→38.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.321 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24367 870 5.1 %RANDOM
Rwork0.18679 ---
all0.24814 181062 --
obs0.18947 20622 84.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.488 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0 Å2
2---0.1 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 0 45 121 1630
LS refinement shellResolution: 1.951→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 24 -
Rwork0.414 288 -
obs--21.88 %

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