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- PDB-1ypn: REDUCED FORM HYDROXYMETHYLBILANE SYNTHASE (K59Q MUTANT) CRYSTAL S... -

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Basic information

Entry
Database: PDB / ID: 1ypn
TitleREDUCED FORM HYDROXYMETHYLBILANE SYNTHASE (K59Q MUTANT) CRYSTAL STRUCTURE AFTER 2 HOURS IN A FLOW CELL DETERMINED BY TIME-RESOLVED LAUE DIFFRACTION
ComponentsHYDROXYMETHYLBILANE SYNTHASE
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: 2.3 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: J.Chem.Soc.,Faraday Trans. / Year: 1998
Title: Time-Resolved Structures of Hydroxymethylbilane Synthase (Lys59Gln Mutant) as It Isloaded with Substrate in the Crystal Determined by Laue Diffraction
Authors: Helliwell, J.R. / Nieh, Y.P. / Cassetta, A. / Habash, J. / Carr, P.D. / Ursby, T. / Wulff, M. / Thompson, A.W. / Niemann, A.C. / Haedener, A.
#1: Journal: Time-Resolved Diffraction (in: Oxford Series on Synchrotron Radiation, V.2)
Year: 1997
Title: Time-Resolved Protein Crystal Diffraction: Determination by the Laue Method of the Behaviour of the Enzyme Hydroxymethylbilane Synthase (Lys59Gln Mutant) as It is Loaded with Substrate in the Crystal
Authors: Helliwell, J.R. / Nieh, Y.P. / Cassetta, A. / Raftery, J. / Haedener, A. / Niemann, A.C. / Battersby, A.R. / Carr, P.D. / Wulff, M. / Ursby, T. / Moy, J.P. / Thompson, A.W.
History
DepositionJun 26, 1998Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Non-polymer description
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYDROXYMETHYLBILANE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3112
Polymers33,8911
Non-polymers4201
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.470, 76.150, 50.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HYDROXYMETHYLBILANE SYNTHASE / PORPHOBILINOGEN DEAMINASE


Mass: 33890.754 Da / Num. of mol.: 1 / Fragment: THREE DOMAINS / Mutation: K59Q
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.: 103 / 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: 2.52 Å3/Da / Density % sol: 50 %
Crystal growpH: 5.3 / Details: pH 5.3
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.4
DetectorDetector: CCD / Date: Nov 1, 1995
RadiationMonochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelengthWavelength: 0.4 Å / Relative weight: 1
ReflectionResolution: 2.3→14.2 Å / Num. obs: 11383 / % possible obs: 72.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 4.9
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.3 / % possible all: 69.5
Reflection shell
*PLUS
% possible obs: 69.5 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DARESBURYLAUE SUITEdata reduction
LAUENORMdata scaling
CCP4(AGROVATA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AH5

1ah5


Resolution: 2.3→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE FOLLOWING REPRESENTS TWO POSSIBLE INTERPRETATIONS FOR THE RESIDUAL DENSITY PEAKS NEAR THE ACTIVE SITE. THESE ATOMS ARE NOT INCLUDED IN THE REFINED ENTRY. ES C1 MPU 317 18.066 7.441 24. ...Details: THE FOLLOWING REPRESENTS TWO POSSIBLE INTERPRETATIONS FOR THE RESIDUAL DENSITY PEAKS NEAR THE ACTIVE SITE. THESE ATOMS ARE NOT INCLUDED IN THE REFINED ENTRY. ES C1 MPU 317 18.066 7.441 24.741 1.00 37.78 C2 MPU 317 18.656 7.598 25.957 1.00 34.85 C3 MPU 317 17.636 7.431 26.931 1.00 34.45 C4 MPU 317 16.462 7.194 26.266 1.00 34.64 C5 MPU 317 20.126 7.927 26.193 1.00 35.91 C6 MPU 317 20.580 9.306 25.663 1.00 37.14 C7 MPU 317 17.812 7.376 28.420 1.00 39.33 C8 MPU 317 17.441 8.637 29.164 1.00 41.42 C9 MPU 317 17.216 8.375 30.652 1.00 44.03 CH MPU 317 18.660 7.490 23.334 1.00 39.78 N1 MPU 317 16.714 7.196 24.934 1.00 35.83 O1 MPU 317 21.627 9.819 26.117 1.00 26.39 O2 MPU 317 19.882 9.874 24.789 1.00 39.95 O3 MPU 317 17.777 7.371 31.189 1.00 41.51 O4 MPU 317 16.457 9.168 31.272 1.00 44.53 N2 MPU 317 18.671 6.176 22.688 1.00 35.23 EP C1 MPU 317 16.744 7.168 25.091 1.00 53.28 C2 MPU 317 18.034 7.174 24.679 1.00 54.37 C3 MPU 317 18.838 7.176 25.840 1.00 52.21 C5 MPU 317 18.501 7.135 23.241 1.00 59.11 C6 MPU 317 18.419 8.470 22.530 1.00 64.68 C7 MPU 317 20.339 7.170 25.898 1.00 49.54 C8 MPU 317 20.913 8.218 26.812 1.00 42.08 C9 MPU 317 20.840 9.587 26.213 1.00 32.97 CH MPU 317 15.457 7.163 24.306 1.00 54.00 N1 MPU 317 16.724 7.163 26.458 1.00 55.05 O1 MPU 317 19.289 9.333 22.797 1.00 65.91 O2 MPU 317 17.479 8.660 21.719 1.00 63.89 O3 MPU 317 21.913 10.194 26.071 1.00 33.28 O4 MPU 317 19.729 10.043 25.874 1.00 30.65 C4 MPU 317 18.012 7.163 26.924 1.00 55.19 N2 MPU 317 14.560 8.204 24.757 1.00 50.26 C1 MPU 318 17.611 7.981 29.348 1.00 60.97 C2 MPU 318 17.362 9.319 29.304 1.00 63.79 C3 MPU 318 16.609 9.638 30.459 1.00 64.74 CH MPU 318 18.352 7.071 28.406 1.00 57.37 N1 MPU 318 17.042 7.467 30.482 1.00 61.70 C4 MPU 318 16.426 8.478 31.164 1.00 63.62 C1 MPU 319 15.396 9.357 33.385 1.00 60.58 C2 MPU 319 14.647 9.451 34.523 1.00 57.45 C3 MPU 319 14.739 10.792 34.976 1.00 58.19 CH MPU 319 15.679 8.177 32.460 1.00 61.22 N1 MPU 319 15.937 10.591 33.129 1.00 59.35 C4 MPU 319 15.537 11.460 34.095 1.00 57.90 C1 MPU 320 17.073 13.274 35.005 1.00 60.74 C2 MPU 320 17.015 13.824 36.250 1.00 61.26 C3 MPU 320 18.349 13.936 36.717 1.00 64.14 C4 MPU 320 19.163 13.453 35.734 1.00 63.20 CH MPU 320 15.988 12.900 34.027 1.00 58.80 N1 MPU 320 18.383 13.052 34.687 1.00 62.92 MPU 318,319,320 HAVE NO SIDE CHAINS MODELLED, DUE TO DISORDER/POOR ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1176 10 %RANDOM
Rwork0.199 ---
obs0.199 11383 72.9 %-
Displacement parametersBiso mean: 22 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 30 103 2357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.671
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.276
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.347 125 10 %
Rwork0.277 1172 -
obs--68.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.276

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