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- PDB-3nrb: Crystal structure of a formyltetrahydrofolate deformylase (purU, ... -

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Basic information

Entry
Database: PDB / ID: 3nrb
TitleCrystal structure of a formyltetrahydrofolate deformylase (purU, PP_1943) from PSEUDOMONAS PUTIDA KT2440 at 2.05 A resolution
ComponentsFormyltetrahydrofolate deformylase
KeywordsHYDROLASE / N-terminal 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 / 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 / Formyl transferase, N-terminal domain / ACT domain / ACT domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / ACT domain profile. / ACT domain / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / IMIDAZOLE / Unknown ligand / Formyltetrahydrofolate deformylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a formyltetrahydrofolate deformylase (purU, PP_1943) from PSEUDOMONAS PUTIDA KT2440 at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
C: Formyltetrahydrofolate deformylase
D: Formyltetrahydrofolate deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,73822
Polymers129,5804
Non-polymers1,15818
Water14,142785
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15790 Å2
ΔGint-27 kcal/mol
Surface area43450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.452, 118.245, 129.193
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A6 - 285
2116B6 - 285
3116C6 - 285
4116D6 - 285
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY INDICATES A TETRAMER IS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Formyltetrahydrofolate deformylase


Mass: 32395.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: purU-3, PP1943, PP_1943 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q88LI9

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Non-polymers , 6 types, 803 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 785 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1.0000M NaCitrate, 0.1M CHES pH 9.5, 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: 0.91837,0.97925,0.97911
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 30, 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
20.979251
30.979111
ReflectionResolution: 2.05→29.961 Å / Num. obs: 79699 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.029 Å2 / Rmerge(I) obs: 0.143 / Rsym value: 0.143 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.05-2.13.70.8041.62197358630.804100
2.1-2.163.70.7151.82131956910.715100
2.16-2.223.80.6062.22082555470.606100
2.22-2.293.80.532.52016453720.53100
2.29-2.373.80.4632.91969952390.463100
2.37-2.453.80.4163.21899250540.416100
2.45-2.543.80.3493.91822548490.349100
2.54-2.653.80.2984.51775247260.298100
2.65-2.763.80.245.41702245330.24100
2.76-2.93.80.1866.81620143120.186100
2.9-3.063.80.13991549141190.139100
3.06-3.243.80.10511.21458838880.10599.9
3.24-3.473.80.082141383436860.08299.9
3.47-3.743.70.0716.51288434380.0799.9
3.74-4.13.70.05619.71185131630.05699.8
4.1-4.583.70.0522.11067428690.0599.7
4.58-5.293.70.05422948625410.05499.5
5.29-6.483.70.05719.8797921630.05799.1
6.48-9.173.60.04621.3620717040.04698.9
9.17-29.963.50.03825.432739420.03895.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
HELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→29.961 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 9.491 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.181
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. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. WATERS WERE EXCLUDED ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.AN UNKNOWN LIGAND HAS BEEN MODELED IN THE STRUCTURE. BASED ON DENSITY AND HYDROGEN BONDING DONOR/ACCEPTOR LOCATIONS, THIS MAY BE NITROBENZENE, BENZOATE, OR NICOTINIC ACID. 5. SODIUM (NA) IONS AND CITRATE (FLC) ANIONS FROM THE CRYSTALLIZATION REAGENT, IMIDAZOLE (IMD) FROM THE PROTEIN BUFFER AND ETHYLENE GLYCOL (EDO) FROM THE CRYOPROTECTANT SOLUTION ARE MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3987 5 %RANDOM
Rwork0.184 ---
obs0.187 79629 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.8 Å2 / Biso mean: 28.05 Å2 / Biso min: 5.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2---1.04 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8777 0 95 785 9657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0229323
X-RAY DIFFRACTIONr_bond_other_d0.0010.026237
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.94512663
X-RAY DIFFRACTIONr_angle_other_deg0.924315120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95751173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27823.273440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.245151511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9721575
X-RAY DIFFRACTIONr_chiral_restr0.0960.21418
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210614
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022021
X-RAY DIFFRACTIONr_mcbond_it2.02235770
X-RAY DIFFRACTIONr_mcbond_other0.5832329
X-RAY DIFFRACTIONr_mcangle_it3.21659344
X-RAY DIFFRACTIONr_scbond_it5.36183553
X-RAY DIFFRACTIONr_scangle_it7.051113319
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3279 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.385
BLOOSE POSITIONAL0.515
CLOOSE POSITIONAL0.55
DLOOSE POSITIONAL0.425
ALOOSE THERMAL2.2810
BLOOSE THERMAL2.9410
CLOOSE THERMAL2.6410
DLOOSE THERMAL2.4210
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 317 -
Rwork0.26 5514 -
all-5831 -
obs--99.73 %
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)
10.17890.02170.10080.6133-0.28150.20.0480.0308-0.0277-0.0016-0.0210.04470.02820.0375-0.0270.02860.02330.00310.02680.00880.022338.075346.53316.0628
20.20050.13790.13530.19890.1060.1933-0.0106-0.01160.0326-0.02440.01490.0608-0.01250.0061-0.00430.03030.01620.00330.02050.01020.033510.485775.65866.659
30.0709-0.08360.0270.4379-0.28720.2165-0.02420.00170.00780.05560.0112-0.0317-0.03740.00010.0130.0497-0.0261-0.01810.01940.00570.015638.818971.173830.2373
40.29870.0820.03040.46890.12070.05630.08320.0054-0.05050.0742-0.0615-0.01740.0041-0.0243-0.02170.0528-0.0135-0.00290.02820.00510.01917.178246.791625.7467
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 286
2X-RAY DIFFRACTION2B5 - 286
3X-RAY DIFFRACTION3C4 - 286
4X-RAY DIFFRACTION4D4 - 286

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