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- PDB-3o1l: Crystal structure of a formyltetrahydrofolate deformylase (PSPTO_... -

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Basic information

Entry
Database: PDB / ID: 3o1l
TitleCrystal structure of a formyltetrahydrofolate deformylase (PSPTO_4314) from Pseudomonas syringae pv. tomato str. DC3000 at 2.20 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 / Formyl transferase, N-terminal domain / ACT domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / ACT domain profile. / ACT domain ...Formyltetrahydrofolate deformylase / Formyltetrahydrofolate deformylase, C-terminal hydrolase domain / Formyltetrahydrofolate deformylase, 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 speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a formyltetrahydrofolate deformylase (PSPTO_4314) from Pseudomonas syringae pv. tomato str. DC3000 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Formyltetrahydrofolate deformylase
B: Formyltetrahydrofolate deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,23319
Polymers70,6322
Non-polymers1,60117
Water5,296294
1
A: Formyltetrahydrofolate deformylase
hetero molecules

B: Formyltetrahydrofolate deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,23319
Polymers70,6322
Non-polymers1,60117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6020 Å2
ΔGint-132 kcal/mol
Surface area27880 Å2
MethodPISA
2
A: Formyltetrahydrofolate deformylase
hetero molecules

A: Formyltetrahydrofolate deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,52122
Polymers70,6322
Non-polymers1,89020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6990 Å2
ΔGint-142 kcal/mol
Surface area29030 Å2
MethodPISA
3
B: Formyltetrahydrofolate deformylase
hetero molecules

B: Formyltetrahydrofolate deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,94516
Polymers70,6322
Non-polymers1,31314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5630 Å2
ΔGint-110 kcal/mol
Surface area26150 Å2
MethodPISA
4
A: Formyltetrahydrofolate deformylase
B: Formyltetrahydrofolate deformylase
hetero molecules

A: Formyltetrahydrofolate deformylase
B: Formyltetrahydrofolate deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,46638
Polymers141,2634
Non-polymers3,20334
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area21530 Å2
ΔGint-310 kcal/mol
Surface area46280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.271, 131.271, 102.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 1 - 283 / Label seq-ID: 20 - 302

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AND A TETRAMER AS PROBABLE OLIGOMERIZATION STATES.

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Components

#1: Protein Formyltetrahydrofolate deformylase


Mass: 35315.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: purU-3, PSPTO4314, PSPTO_4314 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q87X74
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT 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: 3.14 Å3/Da / Density % sol: 60.84 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-MERGE, COMPLETENESS AND
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.57
Details: 1.4500M ammonium sulfate, 12.0000% Glycerol, 0.1M TRIS pH 8.57, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97889
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 11, 2010 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 2.2→29.728 Å / Num. obs: 46149 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.231 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.71
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.2-2.280.8261.9335808829199.8
2.28-2.370.6842.2329508583199.9
2.37-2.480.5212.9341018865199.9
2.48-2.610.3993.7333468648199.8
2.61-2.770.2925.2330658560199.8
2.77-2.980.1897.6332558594199.9
2.98-3.280.10512.8338888751199.9
3.28-3.760.05721.2343798859199.9
3.76-4.720.03631.5335368649199.8
4.72-29.7280.02937.8341558817199.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.728 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 8.277 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.157
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. GLYCEROL (GOL) AND SULFATE MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 2331 5.1 %RANDOM
Rwork0.173 ---
obs0.1745 46089 99.89 %-
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: 121.03 Å2 / Biso mean: 56.8427 Å2 / Biso min: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20 Å2
2---1.53 Å20 Å2
3---3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 93 294 5101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215065
X-RAY DIFFRACTIONr_bond_other_d0.0020.023420
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9336894
X-RAY DIFFRACTIONr_angle_other_deg1.02538256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5055616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11822.734267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70915822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7441547
X-RAY DIFFRACTIONr_chiral_restr0.0980.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215645
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021106
X-RAY DIFFRACTIONr_mcbond_it1.1161.52972
X-RAY DIFFRACTIONr_mcbond_other0.331.51183
X-RAY DIFFRACTIONr_mcangle_it1.99124831
X-RAY DIFFRACTIONr_scbond_it3.27832093
X-RAY DIFFRACTIONr_scangle_it4.8394.52046
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3881 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.460.5
MEDIUM THERMAL1.192
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 170 -
Rwork0.233 3169 -
all-3339 -
obs--99.88 %
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)
11.0712-0.8244-0.0021.09130.11860.5820.12650.21350.2162-0.2571-0.1171-0.1952-0.0120.0958-0.00940.14780.00240.03440.11760.04130.048333.56855.776-13.972
21.0758-0.8224-0.2881.29790.31780.4899-0.1467-0.2473-0.12360.27250.10870.12360.13130.06040.0380.12440.00860.01750.11450.02290.016421.95639.67416.67
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-14 - 283
2X-RAY DIFFRACTION2B-1 - 283

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