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- PDB-3obi: Crystal structure of a formyltetrahydrofolate deformylase (NP_949... -

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Basic information

Entry
Database: PDB / ID: 3obi
TitleCrystal structure of a formyltetrahydrofolate deformylase (NP_949368) from RHODOPSEUDOMONAS PALUSTRIS CGA009 at 1.95 A resolution
ComponentsFormyltetrahydrofolate deformylase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


formyltetrahydrofolate deformylase / formyltetrahydrofolate deformylase activity / 'de novo' IMP biosynthetic process / one-carbon metabolic process
Similarity search - Function
Formyltetrahydrofolate deformylase / Formyltetrahydrofolate deformylase, C-terminal hydrolase domain / Formyltetrahydrofolate deformylase, ACT domain / ACT domain / Formyl transferase, N-terminal domain / ACT domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / ACT domain profile. ...Formyltetrahydrofolate deformylase / Formyltetrahydrofolate deformylase, C-terminal hydrolase domain / Formyltetrahydrofolate deformylase, ACT domain / ACT domain / Formyl transferase, N-terminal domain / ACT domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / ACT domain profile. / ACT domain / ACT-like domain / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Formyltetrahydrofolate deformylase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a formyltetrahydrofolate deformylase (NP_949368) from RHODOPSEUDOMONAS PALUSTRIS CGA009 at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 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
Revision 1.4Nov 27, 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: Formyltetrahydrofolate deformylase
B: Formyltetrahydrofolate deformylase
C: Formyltetrahydrofolate deformylase
D: Formyltetrahydrofolate deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,99033
Polymers132,1904
Non-polymers1,80029
Water18,0331001
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Formyltetrahydrofolate deformylase
D: Formyltetrahydrofolate deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,77813
Polymers66,0952
Non-polymers68311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint19 kcal/mol
Surface area27720 Å2
MethodPISA
3
B: Formyltetrahydrofolate deformylase
C: Formyltetrahydrofolate deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,21220
Polymers66,0952
Non-polymers1,11718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint41 kcal/mol
Surface area27830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.048, 141.111, 77.563
Angle α, β, γ (deg.)90.000, 107.830, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Formyltetrahydrofolate deformylase


Mass: 33047.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: purU, RPA4032 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100
References: UniProt: Q6N2L8, formyltetrahydrofolate deformylase
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1001 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20.0% polyethylene glycol 8000, 0.3M calcium acetate, 0.1M sodium cacodylate pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.90497,0.97939,0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.904971
20.979391
30.979151
ReflectionResolution: 1.95→29.673 Å / Num. all: 101081 / Num. obs: 101081 / % possible obs: 97.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.735 Å2 / Rsym value: 0.108 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-23.50.5831.32525171800.58394.1
2-2.063.50.4721.62470970540.47294.1
2.06-2.123.50.3981.92378968120.39894.1
2.12-2.183.50.3442.22314066560.34494.3
2.18-2.253.40.32.52257665490.395.6
2.25-2.333.40.2592.92195563770.25996
2.33-2.423.40.2143.52124461980.21496.9
2.42-2.523.40.1943.92062259930.19497.7
2.52-2.633.40.1684.42002658350.16899
2.63-2.763.50.1325.51933056010.13299.1
2.76-2.913.50.1166.21869353640.11699.3
2.91-3.083.50.0976.61769250200.09799.2
3.08-3.33.60.0916.81689647380.09199.2
3.3-3.563.60.0747.71617444660.07499.8
3.56-3.93.70.0648.81527940970.064100
3.9-4.363.80.0579.91429437390.057100
4.36-5.033.80.0539.51254932770.053100
5.03-6.173.80.0589.41066027840.058100
6.17-8.723.80.0618.1827421740.061100
8.72-29.6733.70.0558.7429111670.05597.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→29.673 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 8.947 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.184
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTION SOLUTION ARE MODELED. 7. THERE IS SOME UNMODELED DENSITY NEAR RESIDUE 17 IN EACH CHAIN THAT CAN NOT BE ASSIGNED.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 5035 5 %RANDOM
Rwork0.2336 ---
obs0.2358 101028 97.07 %-
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: 73.8 Å2 / Biso mean: 30.989 Å2 / Biso min: 7.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å2-0.38 Å2
2---0.13 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9085 0 116 1001 10202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0219738
X-RAY DIFFRACTIONr_bond_other_d0.0030.026810
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.93613198
X-RAY DIFFRACTIONr_angle_other_deg1.281316384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.94451231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69921.943494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.042151636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.27815113
X-RAY DIFFRACTIONr_chiral_restr0.0990.21454
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210938
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022223
X-RAY DIFFRACTIONr_mcbond_it0.7511.55813
X-RAY DIFFRACTIONr_mcbond_other0.1671.52351
X-RAY DIFFRACTIONr_mcangle_it1.37729449
X-RAY DIFFRACTIONr_scbond_it2.03333925
X-RAY DIFFRACTIONr_scangle_it3.3594.53702
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 356 -
Rwork0.298 6792 -
all-7148 -
obs--93.83 %
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)
10.697-0.2341-0.0532.227-0.63320.8407-0.01350.1845-0.0725-0.21730.0770.2062-0.0324-0.1061-0.06340.06-0.0283-0.01910.1021-0.0310.056-5.53848.04528.276
20.4278-0.0558-0.21.05250.34030.7709-0.03260.04970.0415-0.0330.073-0.06930.04280.0606-0.04040.0381-0.0206-0.00430.04010.01880.033117.25574.96728.652
30.46270.1564-0.23740.8581-0.50870.93290.0078-0.04280.04710.0640.04420.0730.0155-0.0569-0.05190.04510.02220.00160.044-0.02110.0381-5.95874.93858.094
40.68580.26410.02121.94420.56920.9390.0205-0.1716-0.08070.24030.0288-0.2081-0.02380.0566-0.04940.05940.0259-0.02590.09460.03470.064116.9348.03458.471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 287
2X-RAY DIFFRACTION2B3 - 287
3X-RAY DIFFRACTION3C3 - 286
4X-RAY DIFFRACTION4D3 - 286

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