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- PDB-3n0v: Crystal structure of a formyltetrahydrofolate deformylase (PP_032... -

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Basic information

Entry
Database: PDB / ID: 3n0v
TitleCrystal structure of a formyltetrahydrofolate deformylase (PP_0327) from PSEUDOMONAS PUTIDA KT2440 at 2.25 A resolution
ComponentsFormyltetrahydrofolate deformylase
KeywordsHYDROLASE / Formyl transferase / ACT domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


formyltetrahydrofolate deformylase / formyltetrahydrofolate deformylase activity / hydroxymethyl-, formyl- and related transferase activity / 'de novo' IMP biosynthetic process / one-carbon metabolic process
Similarity search - Function
Formyltetrahydrofolate deformylase / Formyltetrahydrofolate deformylase, C-terminal hydrolase domain / Formyl transferase, N-terminal domain / ACT domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich ...Formyltetrahydrofolate deformylase / Formyltetrahydrofolate deformylase, C-terminal hydrolase domain / Formyl transferase, N-terminal domain / ACT domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / 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 putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a formyltetrahydrofolate deformylase (PP_0327) from PSEUDOMONAS PUTIDA KT2440 at 2.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)131,4984
Polymers131,4984
Non-polymers00
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-37 kcal/mol
Surface area47350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.213, 93.965, 97.129
Angle α, β, γ (deg.)90.000, 101.380, 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
1114A6 - 197
2114B6 - 197
3114C6 - 197
4114D6 - 197
1214A203 - 285
2214B203 - 285
3214C203 - 285
4214D203 - 285
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Formyltetrahydrofolate deformylase


Mass: 32874.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: purU-1, PP0327, PP_0327 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q88R07
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O
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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.7655.48THE STRUCTURE WAS PHASED BY MAD METHOD AT 2.9 A RESOLUTION AND REFINED AT 2.25 A RESOLUTION AGAINST A DATASET COLLECTED FROM A DIFFERENT CRYSTAL.
2
Crystal grow
Temperature (K)Crystal-IDMethodDetailspH
2771vapor diffusion, sitting drop, nanodrop0.1860M potassium fluoride 20.4000% polyethylene glycol 3350, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop10.0000% PEG-8000, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K8

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
,0.979081
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.95369
SYNCHROTRONSSRL BL9-220.97922,0.91837
,0.97908
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDFeb 11, 2010Flat mirror (vertical focusing)
MARMOSAIC 325 mm CCD2CCDJul 31, 2009Flat collimating mirror, toroid focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal Si(111) bent monochromator (horizontal focusing)MADMx-ray1
2Double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.953691
20.979221
30.918371
ReflectionResolution: 2.25→42.133 Å / Num. obs: 67847 / % possible obs: 99.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 41.528 Å2 / Rsym value: 0.109

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0073refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.3.15data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→42.133 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 17.955 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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. A MET- ...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. 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3426 5.1 %RANDOM
Rwork0.222 ---
obs0.225 67821 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 136.15 Å2 / Biso mean: 64.366 Å2 / Biso min: 35.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å2-0.22 Å2
2--0.31 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.25→42.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8947 0 0 421 9368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0219297
X-RAY DIFFRACTIONr_bond_other_d0.0010.026292
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.94612644
X-RAY DIFFRACTIONr_angle_other_deg0.811315229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80951143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61223.136472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.364151524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1561579
X-RAY DIFFRACTIONr_chiral_restr0.0650.21372
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021991
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3580 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.260.5
BMEDIUM POSITIONAL0.270.5
CMEDIUM POSITIONAL0.240.5
DMEDIUM POSITIONAL0.220.5
AMEDIUM THERMAL3.492
BMEDIUM THERMAL3.452
CMEDIUM THERMAL4.082
DMEDIUM THERMAL3.932
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 264 -
Rwork0.282 4721 -
all-4985 -
obs--100 %
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)
11.1793-0.60140.2090.9690.03831.01810.0088-0.17510.16040.00740.0575-0.1591-0.11460.222-0.06630.2763-0.0360.08690.1855-0.04790.060684.5447.36338.35
21.1597-0.3398-0.23871.29910.30461.0561-0.0599-0.0672-0.01520.1127-0.01950.21070.2494-0.24120.07950.2812-0.06390.09520.20020.01410.103855.36319.29930.504
30.8944-0.10520.03191.78090.3680.98920.06550.1732-0.0031-0.2727-0.01510.2279-0.2632-0.1984-0.05040.35090.07050.04540.21050.05230.098659.57448.8499.428
41.35190.5347-0.1461.10940.08051.0722-0.00130.1124-0.10330.00570.0743-0.09090.14720.2606-0.0730.28140.06110.08320.1973-0.03310.051589.55220.87413.594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 285
2X-RAY DIFFRACTION1A301 - 431
3X-RAY DIFFRACTION2B6 - 198
4X-RAY DIFFRACTION2B201 - 285
5X-RAY DIFFRACTION2B432 - 539
6X-RAY DIFFRACTION3C6 - 198
7X-RAY DIFFRACTION3C200 - 285
8X-RAY DIFFRACTION3C540 - 632
9X-RAY DIFFRACTION4D6 - 285
10X-RAY DIFFRACTION4D633 - 721

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