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- PDB-1o5h: Crystal structure of formiminotetrahydrofolate cyclodeaminase (TM... -

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Basic information

Entry
Database: PDB / ID: 1o5h
TitleCrystal structure of formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution
ComponentsFormiminotetrahydrofolate cyclodeaminase
KeywordsLYASE / TM1560 / Formiminotetrahydrofolate cyclodeaminase / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homologyFormiminotetrahydrofolate cyclodeaminase monomer, up-and-down helical bundle / Cyclodeaminase/cyclohydrolase / Formimidoyltransferase-cyclodeaminase-like superfamily / Formiminotransferase-cyclodeaminase / catalytic activity / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Serine cycle enzyme, putative
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold
Authors: Xu, Q. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Ambing, E. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / ...Authors: Xu, Q. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Ambing, E. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Hornsby, M. / Jaroszewski, L. / Klock, H.E. / Koesema, E. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Levin, I. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Reyes, R. / Robb, A. / Sims, E. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / von Delft, F. / Wang, X. / West, B. / White, A. / Wolf, G. / Zagnitko, O. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionSep 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.5Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formiminotetrahydrofolate cyclodeaminase
B: Formiminotetrahydrofolate cyclodeaminase


Theoretical massNumber of molelcules
Total (without water)49,6312
Polymers49,6312
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-39 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.704, 71.875, 119.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUVALVAL1AA2 - 8714 - 99
21GLUGLUVALVAL1BB2 - 8714 - 99
32MSEMSEMSEMSE3AA88100
42MSEMSEMSEMSE3BB88100
53LYSLYSLEULEU1AA89 - 176101 - 188
63LYSLYSLEULEU1BB89 - 176101 - 188
74GLUGLUGLUGLU3AA177189
84GLUGLUGLUGLU3BB177189
95GLUGLUSERSER1AA178 - 201190 - 213
105GLUGLUTRPTRP1BB178 - 199190 - 211

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Components

#1: Protein Formiminotetrahydrofolate cyclodeaminase


Mass: 24815.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1560 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X1P6, formimidoyltetrahydrofolate cyclodeaminase
Has protein modificationY

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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: 2.84 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5
Details: 5% PEG-6000, 0.1M citric acid pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1reservoirpH7.9
2150 mM1reservoirNaCl
30.25 mMTCEP1reservoir
412 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.978998
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2002
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978998 Å / Relative weight: 1
ReflectionResolution: 2.6→42 Å / Num. all: 13727 / Num. obs: 13727 / % possible obs: 88.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 64.28 Å2 / Rsym value: 0.108 / Net I/σ(I): 13.3
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 419 / Rsym value: 0.591 / % possible all: 38.5
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 12284 / % possible obs: 97.1 % / Num. measured all: 81783 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.87 Å / % possible obs: 76.5 % / Rmerge(I) obs: 0.47

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA5.0)data scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.9999refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→42 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.891 / SU B: 30.538 / SU ML: 0.273 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.411
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. THE CONFORMATION OF RESIDUES 20-22 (P-T-P) IS SUSPECT, BEING POORLY DEFINED IN EXPERIMENTAL MAPS AND WITH RESIDUAL DIFFERENCE DENSITY IN THE REFINED STRUCTURE, AS WELL AS UNUSUAL PRO ...Details: 1. THE CONFORMATION OF RESIDUES 20-22 (P-T-P) IS SUSPECT, BEING POORLY DEFINED IN EXPERIMENTAL MAPS AND WITH RESIDUAL DIFFERENCE DENSITY IN THE REFINED STRUCTURE, AS WELL AS UNUSUAL PRO PUCKERING PHASES AFTER 2. RESIDUES 88-98 IN SUBUNIT ARE POORLY ORDERED IN SUBUNIT A AND DEVIATE CONSIDERABLY FROM SUBUNIT B; NCS RESTRAINTS WERE KEPT TIGHT HERE, HOWEVER, SINCE LOOSE RESTRAINTS DID NOT IMPROVE RFREE OR THE GEOMETRY. 3. THE TWO C-TERMINAL RESIDUES OF SUBUNIT B WERE DISORDERED OMITTED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.27814 597 4.9 %RANDOM
Rwork0.19927 ---
obs0.20289 11576 97.1 %-
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 mean: 44.593 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20 Å2
2--5.01 Å20 Å2
3----6.69 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 0 0 3045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223086
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9724148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3775396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.80526.17141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.74615590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5721514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022282
X-RAY DIFFRACTIONr_nbd_refined0.2530.21659
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2117
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.23
X-RAY DIFFRACTIONr_mcbond_it2.76332024
X-RAY DIFFRACTIONr_mcangle_it3.61953147
X-RAY DIFFRACTIONr_scbond_it7.71781161
X-RAY DIFFRACTIONr_scangle_it11.859111001
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
1489tight positional0.070.05
9loose positional1.385
1489tight thermal5.5710
9loose thermal11.0510
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.511 39 5.71 %
Rwork0.248 644 -
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)
12.5198-0.59711.22792.4528-0.17772.15190.1312-0.408-0.1461-0.1644-0.1810.29030.2768-1.04190.0498-0.0023-0.08890.04680.3851-0.034-0.053726.39644.09652.691
21.4464-0.30760.03290.91090.15945.35730.0788-0.0276-0.16650.00540.0378-0.04530.49030.1366-0.11670.1621-0.0024-0.0320.0049-0.02660.010644.21636.37554.413
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 20114 - 213
22BB2 - 19914 - 211
Refinement
*PLUS
Num. reflection obs: 12173 / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.46

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