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- PDB-3mw8: Crystal structure of an UROPORPHYRINOGEN-III SYNTHASE (Sama_3255)... -

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Basic information

Entry
Database: PDB / ID: 3mw8
TitleCrystal structure of an UROPORPHYRINOGEN-III SYNTHASE (Sama_3255) from SHEWANELLA AMAZONENSIS SB2B at 1.65 A resolution
ComponentsUroporphyrinogen-III synthase
KeywordsLYASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / HemD-like / heme
Function / homology
Function and homology information


uroporphyrinogen-III synthase / uroporphyrinogen-III synthase activity / uroporphyrinogen III biosynthetic process / protoporphyrinogen IX biosynthetic process
Similarity search - Function
Rossmann fold - #10090 / Tetrapyrrole biosynthesis, uroporphyrinogen III synthase / Tetrapyrrole biosynthesis, uroporphyrinogen III synthase superfamily / Uroporphyrinogen-III synthase / Uroporphyrinogen-III synthase HemD / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uroporphyrinogen-III synthase
Similarity search - Component
Biological speciesShewanella amazonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an UROPORPHYRINOGEN-III SYNTHASE (Sama_3255) from SHEWANELLA AMAZONENSIS SB2B at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uroporphyrinogen-III synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,49813
Polymers25,7531
Non-polymers74512
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.390, 50.073, 58.255
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number4
Space group name H-MP1211
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Uroporphyrinogen-III synthase


Mass: 25752.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella amazonensis (bacteria) / Strain: ATCC BAA-1098 / SB2B / Gene: Sama_3255 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1SAQ1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. CLEAVAGE OF ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. CLEAVAGE OF THE TAG WITH TEV PROTEASE LEAVES ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. HOWEVER, THE CLEAVAGE OF THE TAG WAS INCOMPLETE LEAVING A MIXTURE OF PROTEIN WITH THE INTACT TAG AND CLEAVED TAG.

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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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1500M di-ammonium hydrogen phosphate, 33.0000% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97927
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 11, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.65→38.525 Å / Num. obs: 35551 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.002 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.48
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.710.4422.413207362899.8
1.71-1.780.2993.5132663595100
1.78-1.860.2134.912945348699.8
1.86-1.960.1477.113286360099.9
1.96-2.080.09210.612881348599.9
2.08-2.240.06814.413169355799.8
2.24-2.460.05617.812856347699.5
2.46-2.820.0520.913189361899.5
2.82-3.550.03925.512925354798.5
3.55-38.5250.03627.812299355095.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→38.525 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.519 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.086
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. ETHYLENE GLYCOL (EDO) MODELED ARE PRESENT CRYO SOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1814 5.1 %RANDOM
Rwork0.175 ---
obs0.177 35537 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.07 Å2 / Biso mean: 29.321 Å2 / Biso min: 13.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-1.48 Å2
2---0.86 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 48 226 2044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221920
X-RAY DIFFRACTIONr_bond_other_d0.0020.021328
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9912608
X-RAY DIFFRACTIONr_angle_other_deg0.97733251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0025261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78423.52171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02515321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.581516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212131
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02365
X-RAY DIFFRACTIONr_mcbond_it2.01331228
X-RAY DIFFRACTIONr_mcbond_other0.5963493
X-RAY DIFFRACTIONr_mcangle_it3.06351982
X-RAY DIFFRACTIONr_scbond_it5.0998692
X-RAY DIFFRACTIONr_scangle_it7.54111616
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 132 -
Rwork0.285 2455 -
all-2587 -
obs--99.85 %
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)
12.3301-1.11460.09522.64870.37931.3337-0.0307-0.4272-0.0195-0.1610.21070.022-0.03670.1209-0.17990.0265-0.0194-0.00370.1432-0.01020.0271-3.3407-0.685449.1621
20.7980.49370.41531.84360.51721.2646-0.03870.00460.0298-0.15350.01060.1248-0.00720.05960.0280.04030.0056-0.01220.00750.01260.052919.7132.776424.9658
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 32
2X-RAY DIFFRACTION1A155 - 239
3X-RAY DIFFRACTION2A33 - 154

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