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- PDB-1gtk: Time-resolved and static-ensemble structural chemistry of hydroxy... -

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Basic information

Entry
Database: PDB / ID: 1gtk
TitleTime-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase
ComponentsPORPHOBILINOGEN DEAMINASE
KeywordsTRANSFERASE / BIOSYNTHESIS OF LINEAR TETRAPYRROLE / ALL ALPHA/BETA
Function / homology
Function and homology information


tetrapyrrole biosynthetic process / hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / cytoplasm / cytosol
Similarity search - Function
Porphobilinogen deaminase, C-terminal domain / Porphobilinogen deaminase / Porphobilinogen deaminase, N-terminal / Porphobilinogen deaminase, C-terminal / Porphobilinogen deaminase, dipyrromethane cofactor binding site / Porphobilinogen deaminase, C-terminal domain superfamily / Porphobilinogen deaminase, dipyromethane cofactor binding domain / Porphobilinogen deaminase, C-terminal domain / Porphobilinogen deaminase cofactor-binding site. / Double Stranded RNA Binding Domain ...Porphobilinogen deaminase, C-terminal domain / Porphobilinogen deaminase / Porphobilinogen deaminase, N-terminal / Porphobilinogen deaminase, C-terminal / Porphobilinogen deaminase, dipyrromethane cofactor binding site / Porphobilinogen deaminase, C-terminal domain superfamily / Porphobilinogen deaminase, dipyromethane cofactor binding domain / Porphobilinogen deaminase, C-terminal domain / Porphobilinogen deaminase cofactor-binding site. / Double Stranded RNA Binding Domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DPM / Porphobilinogen deaminase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsHelliwell, J.R. / Nieh, Y.P. / Raftery, J. / Cassetta, A. / Habash, J. / Carr, P.D. / Ursby, T. / Wulff, M. / Thompson, A.W. / Niemann, A.C. / Haedener, A.
Citation
Journal: Faraday Discuss. / Year: 2003
Title: Time-Resolved and Static-Ensemble Structural Chemistry of Hydroxymethylbilane Synthase
Authors: Helliwell, J.R. / Nieh, Y.P. / Habash, J. / Faulder, P.F. / Raftery, J. / Cianci, M. / Wulff, M. / Hadener, A.
#1: Journal: J.Chem.Soc.,Faraday Trans. / Year: 1998
Title: Time-Resolved Structures of Hydroxymethylbilane Synthase (Lys59Gln Mutant) as It is Loaded with Substrate in the Crystal Determined by Laue Diffraction
Authors: Helliwell, J.R. / Nieh, Y.P. / Raftery, J. / Cassetta, A. / Habash, J. / Carr, P.D. / Ursby, T. / Wulff, M. / Thompson, A.W. / Niemann, A.C. / Hadener, A.
History
DepositionJan 16, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 27, 2011Group: Structure summary
Revision 1.3Sep 25, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.4May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 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 / 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 / _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: PORPHOBILINOGEN DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3122
Polymers33,8921
Non-polymers4201
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.500, 75.900, 50.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2056-

HOH

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Components

#1: Protein PORPHOBILINOGEN DEAMINASE / HYDROXYMETHYLBILANE SYNTHASE / PBG / HMBS / HYDROXYMETHYLBILANE SYNTHASE / PRE-UROPORPHYRINOGEN SYNTHASE


Mass: 33891.805 Da / Num. of mol.: 1 / Fragment: THREE DOMAINS
Source method: isolated from a genetically manipulated source
Details: CONTAINS A DIPYRROMETHANE COFACTOR LINKED TO CYSTEINE 242
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P06983, hydroxymethylbilane synthase
#2: Chemical ChemComp-DPM / 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid / DIPYRROMETHANE COFACTOR


Mass: 420.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N2O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.45 Å3/Da / Density % sol: 50 %
Description: THE STRUCTURE WAS ALREADY DETERMINED BUT REFINED HERE ONLY
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.3
Details: PROTEIN WAS CRYSTALLISED AT PH 5.3 IN SITTING DROPS OF 0.05 ML WITH 6-7 MG/ML OF PROTEIN, 0.3 MM EDTA, 15 MM DITHIOTHREITOL, 10%(W/V) PEG6000 AND 0.01% NAN3 IN 0.1 M SODIUM ACETATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.8611
DetectorDetector: CCD / Date: Jun 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8611 Å / Relative weight: 1
ReflectionResolution: 1.66→43.85 Å / Num. obs: 34417 / % possible obs: 87 %
Reflection shellResolution: 1.66→1.75 Å / % possible all: 70.7

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
Ophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YPN

2ypn


Resolution: 1.66→43.85 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.946 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ASYMMETRIC UNIT OF THIS STRUCTURE IS NOT COMPLETE.RESIDUES 1-2, 43-59 ARE MISSING IN THE ENTRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1709 5 %RANDOM
Rwork0.198 ---
obs0.2 32708 87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.66→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 30 320 2578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0212287
X-RAY DIFFRACTIONr_bond_other_d0.0010.022164
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg2.0041.9953099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.9834999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1170.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022573
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02435
X-RAY DIFFRACTIONr_nbd_refined0.2810.3484
X-RAY DIFFRACTIONr_nbd_other0.2180.32062
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5202
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1410.52
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3040.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.324
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.519
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1741.51458
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98222329
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.143829
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7044.5770
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
LS refinement shellResolution: 1.66→1.7 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 67
Rwork0.23 1555
Refinement TLS params.Method: refined / Origin x: 17.4635 Å / Origin y: -1.097 Å / Origin z: 21.7791 Å
111213212223313233
T0.023 Å20.0057 Å20.0077 Å2-0.0244 Å2-0.0093 Å2--0.008 Å2
L0.1975 °2-0.0705 °20.119 °2-0.8669 °2-0.2144 °2--0.2831 °2
S0.0002 Å °0.0056 Å °0.0049 Å °0.0502 Å °0.0089 Å °-0.0016 Å °-0.0099 Å °0.012 Å °-0.009 Å °

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