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- PDB-8pnd: The ES3 intermediate of hydroxymethylbilane synthase R167Q variant -

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Basic information

Entry
Database: PDB / ID: 8pnd
TitleThe ES3 intermediate of hydroxymethylbilane synthase R167Q variant
ComponentsPorphobilinogen deaminase
KeywordsTRANSFERASE / hydroxymethylbilane synthase / HMBS / porphobilinogen deaminase / PBGD / hydroxymethylbilane / porphobilinogen / haem biosynthesis / porphyria / acute intermittent porphyria
Function / homology
Function and homology information


hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / cytoplasm / cytosol
Similarity search - Function
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.
Similarity search - Domain/homology
Chem-ZWW / Porphobilinogen deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSaeter, M.C. / Bustad, H.J. / Laitaoja, M. / Janis, J. / Martinez, A. / Aarsand, A.K. / Kallio, J.P.
Funding support Norway, 2items
OrganizationGrant numberCountry
Other government Norway
Other governmentF-12142 Norway
CitationJournal: Febs J. / Year: 2024
Title: One ring closer to a closure: the crystal structure of the ES 3 hydroxymethylbilane synthase intermediate.
Authors: Bustad, H.J. / Christie, M.S. / Laitaoja, M. / Aarsand, A.K. / Martinez, A. / Janis, J. / Kallio, J.P.
History
DepositionJun 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Porphobilinogen deaminase
B: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,58210
Polymers79,9932
Non-polymers2,5898
Water4,846269
1
A: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3215
Polymers39,9971
Non-polymers1,3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2615
Polymers39,9971
Non-polymers1,2644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.600, 81.136, 192.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Porphobilinogen deaminase / PBG-D / Hydroxymethylbilane synthase / HMBS / Pre-uroporphyrinogen synthase


Mass: 39996.641 Da / Num. of mol.: 2 / Mutation: R167Q (on reference seq P08397)
Source method: isolated from a genetically manipulated source
Details: MGSSHHHHHHSSG = His-tag and linker GENLYFQG = TEV cleavage site MGSSHHHHHHSSGGENLYFQG can be annotated EXPRESSION TAG Numbering on structure starts from Met18 that is corresponding to ...Details: MGSSHHHHHHSSG = His-tag and linker GENLYFQG = TEV cleavage site MGSSHHHHHHSSGGENLYFQG can be annotated EXPRESSION TAG Numbering on structure starts from Met18 that is corresponding to reference sequence P08397 R167Q mutation on the sequence P08397
Source: (gene. exp.) Homo sapiens (human) / Gene: HMBS, PBGD, UPS / Production host: Escherichia coli (E. coli) / References: UniProt: P08397, hydroxymethylbilane synthase
#2: Chemical ChemComp-ZWW / 3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 1048.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C50H57N5O20 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: PEG 3350, Ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03323 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 1.9→43.56 Å / Num. obs: 66997 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 44.91 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04154 / Rpim(I) all: 0.01623 / Net I/σ(I): 22.5
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 1.492 / Num. unique obs: 6596 / CC1/2: 0.627 / Rpim(I) all: 0.5688 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.56 Å / SU ML: 0.2362 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9216
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2166 3421 5.11 %
Rwork0.1855 63564 -
obs0.1872 66985 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.79 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5061 0 182 269 5512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725359
X-RAY DIFFRACTIONf_angle_d0.81657258
X-RAY DIFFRACTIONf_chiral_restr0.0543816
X-RAY DIFFRACTIONf_plane_restr0.007948
X-RAY DIFFRACTIONf_dihedral_angle_d13.8462086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.4091370.36262610X-RAY DIFFRACTION99.93
1.93-1.960.33031390.31912617X-RAY DIFFRACTION99.96
1.96-1.990.27671420.28982644X-RAY DIFFRACTION99.93
1.99-2.020.27161370.26212567X-RAY DIFFRACTION99.93
2.02-2.050.28131450.25742622X-RAY DIFFRACTION100
2.05-2.090.28241340.25342630X-RAY DIFFRACTION99.89
2.09-2.130.25461310.24642643X-RAY DIFFRACTION100
2.13-2.170.271340.25142596X-RAY DIFFRACTION99.82
2.18-2.220.30231460.23622623X-RAY DIFFRACTION99.57
2.22-2.270.24881240.21922627X-RAY DIFFRACTION99.53
2.27-2.330.25751300.20612641X-RAY DIFFRACTION99.32
2.33-2.390.23861420.20022610X-RAY DIFFRACTION100
2.39-2.460.26731280.20532662X-RAY DIFFRACTION99.96
2.46-2.540.27151110.21272675X-RAY DIFFRACTION99.96
2.54-2.630.25511300.21132633X-RAY DIFFRACTION99.82
2.63-2.740.26431580.21442621X-RAY DIFFRACTION99.89
2.74-2.860.2841610.22652643X-RAY DIFFRACTION99.93
2.86-3.020.26041590.19682641X-RAY DIFFRACTION100
3.02-3.20.22021600.19232645X-RAY DIFFRACTION99.82
3.2-3.450.21700.19252621X-RAY DIFFRACTION99.36
3.45-3.80.20351430.17022693X-RAY DIFFRACTION100
3.8-4.350.18741350.14562710X-RAY DIFFRACTION99.89
4.35-5.480.17481480.14392749X-RAY DIFFRACTION99.86
5.48-43.560.18961770.17452841X-RAY DIFFRACTION99.28
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)
15.74019663482-0.0368605105508-1.039086292053.56223405531-1.168128438173.69323271189-0.3322260284690.197751428167-0.242346361633-0.1805390149310.226939075761-0.03721636337750.4766825343090.3202413512060.004892074123990.412538849690.0833063327024-0.02838712446770.247140748668-0.08941965688610.46467414238216.448338694117.9255075229239.199821433
28.242271595871.64031655927-2.05526075243.22811236127-1.29484203796.756472323840.2593507638990.3365556479380.44374215106-0.2833690179-0.190715206267-0.304091078615-0.04311537055151.000649226950.07810996672570.3830854201810.1037222497940.02670668981020.479423210055-0.07278500120810.45836436430918.577195213124.6340062769231.942338215
31.384304699861.080554841280.3870531793951.256140455241.232429103213.49817353875-0.0147750781043-0.122700012416-0.09598113012720.09976460871860.120320695713-0.001185845025420.2078217636630.830162107014-0.1596329622230.3366576826490.08607662976190.01068209544820.498865152842-0.04854374441990.39417259544621.526712392636.4953941427249.207205678
42.002431027161.377248430510.2572375200866.163476826061.076817903951.91136904491-0.05823431035960.06994011850250.1095667296110.08402746623210.1067069804960.499878565267-0.1328396683440.0662924162628-0.03745845380730.2859028805880.02317806869570.02847447301870.2171669211690.03101723633510.3824367687074.0979216202240.732325094241.223467619
54.0241968142-0.686465589979-0.03007925675562.59305856975-1.469621839581.11608171978-0.07841711589490.08778416317090.765352831712-0.4593889347840.3352304722760.000915212508467-2.092188489230.351692636272-0.1729624510711.200446078910.04426649843520.06824616850640.5100755503380.1092322108110.56514246118937.376232574322.4037840228179.649433615
61.08586223357-0.6770764661571.715895979812.08473008503-0.2351358118288.260787761660.1806428724890.1617418665150.195741288831-0.292742249278-0.00908205292851-0.207461982573-0.869087332374-0.0490330587647-0.07282137946220.4730816680750.08921491890540.1104088791380.4720728532690.1513601744710.48407786106638.524872002316.8113356087202.293270517
70.887163302304-0.02337398289531.186999679751.630525168351.003587274557.814363470210.171613606554-0.2252740065370.118560538013-0.0626403830856-0.1134047024480.335418837187-0.751215599494-1.85157638548-0.07975116541970.5953560419170.3727143493720.06937031417381.106508761060.2241640158730.59440874392521.944490267217.3933908587196.418598231
82.53912690247-0.212441532547-0.8895296000484.13574389481-0.6412927967481.80711747995-0.1167087620910.184680506635-0.0467147188082-0.639569177304-0.01996008115030.738291324828-0.605041855793-2.34061997807-0.0307053257480.6898082961250.644888649704-0.02798500984761.713662010320.2557671046760.747542650115.892007993319.944558978192.525093507
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 18 through 45 )AA18 - 451 - 28
22chain 'A' and (resid 46 through 86 )AA46 - 8629 - 58
33chain 'A' and (resid 87 through 228 )AA87 - 22859 - 200
44chain 'A' and (resid 229 through 357 )AA229 - 357201 - 329
55chain 'B' and (resid 18 through 99 )BF18 - 991 - 68
66chain 'B' and (resid 100 through 228 )BF100 - 22869 - 197
77chain 'B' and (resid 229 through 295 )BF229 - 295198 - 264
88chain 'B' and (resid 296 through 357 )BF296 - 357265 - 326

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