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- PDB-3lou: Crystal structure of Formyltetrahydrofolate deformylase (YP_10525... -

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Basic information

Entry
Database: PDB / ID: 3lou
TitleCrystal structure of Formyltetrahydrofolate deformylase (YP_105254.1) from BURKHOLDERIA MALLEI ATCC 23344 at 1.90 A resolution
ComponentsFormyltetrahydrofolate deformylase
KeywordsHYDROLASE / Formyltetrahydrofolate deformylase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


hydroxymethyl-, formyl- and related transferase activity / 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-like domain / Alpha-Beta Plaits ...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-like domain / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Unknown ligand / Formyltetrahydrofolate deformylase / Formyltetrahydrofolate deformylase
Similarity search - Component
Biological speciesBurkholderia mallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Formyltetrahydrofolate deformylase (YP_105254.1) from BURKHOLDERIA MALLEI ATCC 23344 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 1.5Oct 30, 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

Downloads & links

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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)136,04047
Polymers132,7174
Non-polymers3,32343
Water15,655869
1


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


Theoretical massNumber of molelcules
Total (without water)68,16626
Polymers66,3582
Non-polymers1,80824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-50 kcal/mol
Surface area25490 Å2
MethodPISA
3
C: Formyltetrahydrofolate deformylase
D: Formyltetrahydrofolate deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,87421
Polymers66,3582
Non-polymers1,51519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-59 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.628, 93.476, 98.802
Angle α, β, γ (deg.)90.000, 95.290, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A7 - 291
2114B7 - 291
3114C7 - 291
4114D7 - 291
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Formyltetrahydrofolate deformylase


Mass: 33179.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia mallei (bacteria) / Strain: ATCC 23344 / Gene: purU-2, BMAA0482 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100
References: UniProt: Q62DH4, UniProt: A0A0H2WCF8*PLUS, formyltetrahydrofolate deformylase

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Non-polymers , 5 types, 912 molecules

#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 869 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsSEQUENCE THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2000M Li2SO4, 10.0000% PEG-3000, 0.1M Imidazole pH 8.0, 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: 0.91837,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 31, 2009 / 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
10.918371
20.979221
ReflectionResolution: 1.9→29.488 Å / Num. obs: 105637 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.053 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.73
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.970.5541.53923920680195.8
1.97-2.050.3842.23999820862199.1
2.05-2.140.28133837719967198.9
2.14-2.250.2163.73894820244198.8
2.25-2.390.1674.73995220677198.9
2.39-2.580.1345.74126121309198.8
2.58-2.840.09184005920654198.5
2.84-3.250.0611.73986120488198.2
3.25-4.080.04173914320076197.1
4.08-29.4880.03320.23981020337196.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.488 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 7.289 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.137
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.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. 4. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED INTO THE STRUCTURE. 5. SULFATE (SO4),POLYETHYLENE GLYCOL, AND ETHYLENE GLYCOL FROM THE CRYSTALLIZATION/CRYOGENIC CONDITIONS HAVE BEEN MODELED INTO THE STRUCTURE. 6. ELECTRON DENSITIES BETWEEN RESIDUES 62-65 ON THE A AND C SUBUNITS, AND 61-65 ON THE B AND D SUBUNITS ARE DISORDERED; THEREFORE, THESE RESIDUES WERE NOT MODELED. BULK SOLVENT MODELLING. METHOD USED : BABINET MODEL WITH MASK PARAMETERS FOR MASK CALCULATION VDW PROBE RADIUS : 1.40 ION PROBE RADIUS : 0.80 SHRINKAGE RADIUS : 0.80
RfactorNum. reflection% reflectionSelection details
Rfree0.221 5276 5 %RANDOM
Rwork0.185 ---
obs0.187 105611 99.34 %-
Displacement parametersBiso max: 75.91 Å2 / Biso mean: 26.272 Å2 / Biso min: 10.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-0.1 Å2
2--0.88 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8875 0 206 869 9950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229663
X-RAY DIFFRACTIONr_bond_other_d0.0020.026700
X-RAY DIFFRACTIONr_angle_refined_deg1.311.95513142
X-RAY DIFFRACTIONr_angle_other_deg0.781316194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.25451233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.86322.463475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.341151591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.38115101
X-RAY DIFFRACTIONr_chiral_restr0.0690.21468
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022130
X-RAY DIFFRACTIONr_mcbond_it1.05625792
X-RAY DIFFRACTIONr_mcbond_other0.2922310
X-RAY DIFFRACTIONr_mcangle_it1.92349410
X-RAY DIFFRACTIONr_scbond_it3.03863871
X-RAY DIFFRACTIONr_scangle_it4.52983674
Refine LS restraints NCS

Ens-ID: 1 / Number: 3297 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.540.5
2BMEDIUM POSITIONAL0.530.5
3CMEDIUM POSITIONAL0.510.5
4DMEDIUM POSITIONAL0.530.5
1AMEDIUM THERMAL0.952
2BMEDIUM THERMAL0.922
3CMEDIUM THERMAL0.922
4DMEDIUM THERMAL0.922
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 368 -
Rwork0.245 7193 -
all-7561 -
obs--97 %
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)
10.83920.0511-0.05080.8870.02870.47180.0170.09880.0998-0.04510.02070.1163-0.0908-0.1365-0.03770.05480.01860.00560.07470.04820.063317.566-0.38412.455
20.98650.203-0.06381.01960.30150.8793-0.00550.0659-0.10810.07240.0732-0.09130.16080.1842-0.06760.05620.0319-0.01270.0639-0.02370.039547.347-27.91613.131
30.8285-0.1157-0.04140.794-0.05320.6693-0.0055-0.0202-0.07420.02920.06360.15580.0858-0.188-0.05810.0437-0.0181-0.00850.08780.05030.07215.55-29.36633.515
41.0932-0.30240.11370.99890.15280.6281-0.0067-0.12730.1453-0.03320.0529-0.1028-0.13970.0797-0.04630.0699-0.00960.0150.0333-0.02250.042445.32-2.30938.178
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 291
2X-RAY DIFFRACTION2B8 - 291
3X-RAY DIFFRACTION3C7 - 291
4X-RAY DIFFRACTION4D8 - 291

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