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- PDB-3jzv: Crystal structure of Rru_A2000 from Rhodospirillum rubrum: A cupi... -

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Basic information

Entry
Database: PDB / ID: 3jzv
TitleCrystal structure of Rru_A2000 from Rhodospirillum rubrum: A cupin-2 domain.
Componentsuncharacterized protein Rru_A2000
Keywordsstructural genomics / unknown function / cupin-2 fold / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


S-methyl-1-thioxylulose 5-phosphate methylthiotransferase / : / L-methionine salvage from methylthioadenosine / transferase activity / lyase activity / metal ion binding
Similarity search - Function
Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / 1-methylthio-D-xylulose 5-phosphate methylsulfurylase
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Rru_A2000 from Rhodospirillum rubrum: A cupin-2 domain.
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionSep 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein Rru_A2000
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6502
Polymers18,5951
Non-polymers551
Water21612
1
A: uncharacterized protein Rru_A2000
hetero molecules

A: uncharacterized protein Rru_A2000
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3004
Polymers37,1902
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2530 Å2
ΔGint-37 kcal/mol
Surface area15120 Å2
MethodPISA
2
A: uncharacterized protein Rru_A2000
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)111,90012
Polymers111,5706
Non-polymers3306
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area15960 Å2
ΔGint-152 kcal/mol
Surface area37000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.886, 90.886, 161.252
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein uncharacterized protein Rru_A2000


Mass: 18595.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Strain: ATCC 11170 / Description: BC-pSGX4(BC) / Gene: Rru_A2000 / Plasmid: plasmid / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2RSU5
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.45 Å3/Da / Density % sol: 64.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15 % MPD, 0.1M Sodium Hepes pH 7.5, 0.8M Potassium Sodium Tartrate tetrahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-E10.9793
SYNCHROTRONNSLS X29A20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 2, 2009
ADSC QUANTUM 3152CCDJan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.9791
ReflectionResolution: 2.3→25 Å / Num. obs: 11778 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.106 / Χ2: 1.734 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.347.30.4165680.9141100
2.34-2.387.20.335810.9591100
2.38-2.437.20.2915880.8861100
2.43-2.487.20.2855770.9711100
2.48-2.537.20.2335811.0391100
2.53-2.597.20.2035841.051100
2.59-2.657.20.185781.1481100
2.65-2.737.10.1685821.321100
2.73-2.817.10.1495861.4811100
2.81-2.970.1345871.6141100
2.9-370.1235871.8071100
3-3.1270.1075821.9011100
3.12-3.2670.1065932.0581100
3.26-3.4370.1085882.331100
3.43-3.656.90.15862.3641100
3.65-3.936.80.1095892.443199.8
3.93-4.326.90.0995962.519199.8
4.32-4.946.70.0966012.649199.8
4.94-6.216.50.096172.6461100
6.21-256.20.0976272.874198

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→23.58 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.306 / WRfactor Rwork: 0.248 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.751 / SU B: 7.613 / SU ML: 0.181 / SU R Cruickshank DPI: 0.222 / SU Rfree: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.278 560 4.8 %RANDOM
Rwork0.225 ---
obs0.227 11648 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 102.69 Å2 / Biso mean: 60.11 Å2 / Biso min: 39.55 Å2
Baniso -1Baniso -2Baniso -3
1-4.19 Å22.1 Å20 Å2
2--4.19 Å20 Å2
3----6.29 Å2
Refinement stepCycle: LAST / Resolution: 2.3→23.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 1 12 1151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211176
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9431599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4665148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64622.32156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69115170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0391511
X-RAY DIFFRACTIONr_chiral_restr0.0970.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021933
X-RAY DIFFRACTIONr_mcbond_it0.9061.5736
X-RAY DIFFRACTIONr_mcangle_it1.70521167
X-RAY DIFFRACTIONr_scbond_it2.1573440
X-RAY DIFFRACTIONr_scangle_it3.5344.5431
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 52 -
Rwork0.316 799 -
all-851 -
obs--100 %

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