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- PDB-2jcb: The crystal structure of 5-formyl-tetrahydrofolate cycloligase fr... -

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Basic information

Entry
Database: PDB / ID: 2jcb
TitleThe crystal structure of 5-formyl-tetrahydrofolate cycloligase from Bacillus anthracis (BA4489)
Components5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE FAMILY PROTEIN
KeywordsLIGASE / FOLATE METABOLISM
Function / homology
Function and homology information


5-formyltetrahydrofolate cyclo-ligase / 5-formyltetrahydrofolate cyclo-ligase activity / ATP binding / metal ion binding
Similarity search - Function
NagB/RpiA/CoA transferase-like / 5-formyltetrahydrofolate cyclo-ligase / 5-formyltetrahydrofolate cyclo-ligase family / 5-formyltetrahydrofolate cyclo-ligase-like domain superfamily / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / 5-formyltetrahydrofolate cyclo-ligase / 5-formyltetrahydrofolate cyclo-ligase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMeier, C. / Carter, L.G. / Winter, G. / Owens, R.J. / Stuart, D.I. / Esnouf, R.M. / Oxford Protein Production Facility (OPPF) / Structural Proteomics in Europe (SPINE)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Structure of 5-Formyltetrahydrofolate Cyclo-Ligase from Bacillus Anthracis (Ba4489).
Authors: Meier, C. / Carter, L.G. / Winter, G. / Owens, R.J. / Stuart, D.I. / Esnouf, R.M.
History
DepositionDec 21, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 6, 2015Group: Source and taxonomy
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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_conn.ptnr2_label_seq_id / _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_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: 5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE FAMILY PROTEIN
B: 5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9378
Polymers46,8442
Non-polymers1,0936
Water5,837324
1
A: 5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9684
Polymers23,4221
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9684
Polymers23,4221
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.152, 45.499, 66.999
Angle α, β, γ (deg.)74.92, 78.01, 70.14
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUASNASNAA4 - 7912 - 87
21GLUGLUASNASNBB4 - 7912 - 87
12ARGARGLEULEUAA83 - 11091 - 118
22ARGARGLEULEUBB83 - 11091 - 118
13GLUGLUVALVALAA113 - 169121 - 177
23GLUGLUVALVALBB113 - 169121 - 177
14ASPASPVALVALAA173 - 187181 - 195
24ASPASPVALVALBB173 - 187181 - 195

NCS oper: (Code: given
Matrix: (-0.67169, -0.74017, -0.03141), (-0.73997, 0.66825, 0.07673), (-0.0358, 0.07478, -0.99656)
Vector: 46.944, 46.062, 33.117)

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Components

#1: Protein 5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE FAMILY PROTEIN / 5-FORMYL-TETRAHYDROFOLATE CYCLOLIGASE


Mass: 23421.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Plasmid: GATEWAY / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA PLYSS
References: UniProt: Q81LX0, UniProt: A0A6L8PZ12*PLUS, 5-formyltetrahydrofolate cyclo-ligase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsM1V IS A CLONING ARTEFACT.

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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: 2.19 Å3/Da / Density % sol: 44 %
Crystal growpH: 5.5
Details: 3.8MM FOLINATE, 3.8MM ATP, 30MM MAGNESIUM CHLORIDE, 25% POLYETHYLENE GLYCOL 3350, 100 MM BIS-TRIS (PH 5.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 49797 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.9 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YDM

1ydm


Resolution: 1.6→18.69 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.254 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2491 5 %RANDOM
Rwork0.189 ---
obs0.192 47297 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.68 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→18.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 66 324 3558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223299
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9824462
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.895382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8124.188160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42315618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8051522
X-RAY DIFFRACTIONr_chiral_restr0.1080.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022436
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.21491
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22234
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0921.51983
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56923120
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.46731523
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.564.51342
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
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
704medium positional0.170.5
737loose positional0.545
704medium thermal2.5710
737loose thermal2.820
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 173
Rwork0.28 3468
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)
12.1426-0.00260.33442.7626-0.75043.1718-0.0378-0.1080.11190.2667-0.00140.066-0.1970.02090.0393-0.1816-0.0047-0.0239-0.2215-0.0435-0.156637.14231.85591.1883
22.8831-0.4751-2.04342.2442-0.297.65170.13970.24280.1695-0.2397-0.2152-0.126-0.3643-0.16830.0754-0.14510.0155-0.0043-0.10230.0181-0.132921.011519.724930.6753
331.862.782612.21188.6778-3.805810.12660.4947-1.2897-0.22811.1515-0.3310.306-0.7649-0.0755-0.16370.0872-0.1253-0.0509-0.1554-0.1371-0.168142.543112.686110.8301
48.96494.9809-11.96715.8201-8.512617.1126-0.93010.55280.2202-1.60771.09640.9435-1.1018-2.3021-0.16630.0130.1364-0.12080.28580.11290.04138.310623.547521.9061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 189
2X-RAY DIFFRACTION2B-1 - 187
3X-RAY DIFFRACTION3A1190
4X-RAY DIFFRACTION4B1189

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