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- PDB-2vd3: The structure of histidine inhibited HisG from Methanobacterium t... -

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Basic information

Entry
Database: PDB / ID: 2vd3
TitleThe structure of histidine inhibited HisG from Methanobacterium thermoautotrophicum
ComponentsATP PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / METAL-BINDING / GLYCOSYLTRANSFERASE / HISG / HISTIDINE / MAGNESIUM / HISTIDINE BIOSYNTHESIS / AMINO-ACID BIOSYNTHESIS / ATP PHOSPHORIBOSYL TRANSFERASE
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
ATP phosphoribosyltransferase HisG, long form / Histidine biosynthesis HisG, C-terminal / HisG, C-terminal domain / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta ...ATP phosphoribosyltransferase HisG, long form / Histidine biosynthesis HisG, C-terminal / HisG, C-terminal domain / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / IMIDAZOLE / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesMETHANOBACTERIUM THERMOAUTOTROPHICUM (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.45 Å
AuthorsLohkamp, B. / Schweikert, T. / Lapthorn, A.J.
CitationJournal: To be Published
Title: The Structure of Histidine Inhibited Hisg from Methanobacterium Thermoautotrophicum
Authors: Lohkamp, B. / Schweikert, T. / Lapthorn, A.J.
History
DepositionSep 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: 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 / struct_conn / struct_ncs_dom_lim
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 / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP PHOSPHORIBOSYLTRANSFERASE
B: ATP PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,44431
Polymers62,6782
Non-polymers1,76629
Water91951
1
A: ATP PHOSPHORIBOSYLTRANSFERASE
B: ATP PHOSPHORIBOSYLTRANSFERASE
hetero molecules

A: ATP PHOSPHORIBOSYLTRANSFERASE
B: ATP PHOSPHORIBOSYLTRANSFERASE
hetero molecules

A: ATP PHOSPHORIBOSYLTRANSFERASE
B: ATP PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,33393
Polymers188,0346
Non-polymers5,29987
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
Buried area30800 Å2
ΔGint-158.3 kcal/mol
Surface area82760 Å2
MethodPQS
Unit cell
Length a, b, c (Å)112.103, 112.103, 247.622
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1295-

MG

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 1 - 287 / Label seq-ID: 3 - 289

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATP PHOSPHORIBOSYLTRANSFERASE / ATP-PRTASE / ATP-PRT


Mass: 31338.990 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOBACTERIUM THERMOAUTOTROPHICUM (archaea)
Strain: DELTAH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O27550, ATP phosphoribosyltransferase

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Non-polymers , 7 types, 80 molecules

#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 46.97 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Type: SRS / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 10000 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.05

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.45→45 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 23.662 / SU ML: 0.264 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 2.483 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1687 8.4 %RANDOM
Rwork0.226 ---
obs0.231 18465 90 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20.8 Å20 Å2
2--1.6 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 2.45→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 103 51 4536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224535
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1592.0016154
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4675580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.39323.661183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71515796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3281542
X-RAY DIFFRACTIONr_chiral_restr0.0770.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023321
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.22003
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23116
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2191
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.2131
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3861.52977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.68424698
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.84931685
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4474.51454
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 / Number: 2131 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.370.5
medium thermal0.32
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.471 87
Rwork0.333 977
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.94870.49250.97333.27561.27922.8377-0.117-0.0267-0.08850.00350.1273-0.1351-0.0690.3121-0.0103-0.1427-0.02990.0634-0.19890.0616-0.096448.679278.899180.8581
21.48850.35981.50250.99710.63343.7199-0.0167-0.28390.09510.0630.00280.1772-0.2323-0.43880.0139-0.15530.02430.1158-0.0850.0606-0.056534.916896.083585.069
32.4407-0.3126-1.08664.0527-1.28053.390.07410.14210.1944-0.00690.05370.2097-0.2755-0.1711-0.1278-0.1209-0.056-0.0254-0.00020.0121-0.078337.750589.222840.9517
40.75520.3945-0.80791.5818-1.84873.3337-0.01910.096-0.2244-0.1575-0.0509-0.0380.18250.12250.07-0.09150.0069-0.0253-0.1813-0.0914-0.029455.172676.154337.0391
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 90
2X-RAY DIFFRACTION1A179 - 212
3X-RAY DIFFRACTION2A91 - 178
4X-RAY DIFFRACTION2A213 - 287
5X-RAY DIFFRACTION3B0 - 90
6X-RAY DIFFRACTION3B179 - 212
7X-RAY DIFFRACTION4B91 - 177
8X-RAY DIFFRACTION4B213 - 287

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