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- PDB-7cd0: Crystal structure of the 2-iodoporphobilinogen-bound ES2 intermed... -

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Basic information

Entry
Database: PDB / ID: 7cd0
TitleCrystal structure of the 2-iodoporphobilinogen-bound ES2 intermediate form of human hydroxymethylbilane synthase
ComponentsPorphobilinogen deaminase
KeywordsTRANSFERASE / Porphyrin synthesis
Function / homology
Function and homology information


hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / heme O biosynthetic process / heme A biosynthetic process / heme B 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-7J8 / Chem-FWL / Porphobilinogen deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsSato, H. / Sugishima, M. / Wada, K. / Hirabayashi, K. / Tsukaguchi, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24550201 Japan
Japan Society for the Promotion of Science (JSPS)15K07018 Japan
Japan Society for the Promotion of Science (JSPS)18K05326 Japan
CitationJournal: Biochem.J. / Year: 2021
Title: Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps.
Authors: Sato, H. / Sugishima, M. / Tsukaguchi, M. / Masuko, T. / Iijima, M. / Takano, M. / Omata, Y. / Hirabayashi, K. / Wada, K. / Hisaeda, Y. / Yamamoto, K.
History
DepositionJun 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,7965
Polymers78,7662
Non-polymers2,0303
Water1,36976
1
A: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2222
Polymers39,3831
Non-polymers8391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5743
Polymers39,3831
Non-polymers1,1912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.416, 81.366, 108.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain "A" and (resid 19 through 57 or resid 77...
21(chain "B" and ((resid 19 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
111ARGSERA1 - 39
121PHELEUA42 - 322
211ARGLEUB1 - 320

NCS oper: (Code: givenMatrix: (-0.999902136534, 0.00805956958056, -0.0114350641629), (0.00869743554692, 0.998343438805, -0.0568747115119), (0.0109577355846, -0.0569686012891, -0.998315835043)Vector: - ...NCS oper: (Code: given
Matrix: (-0.999902136534, 0.00805956958056, -0.0114350641629), (0.00869743554692, 0.998343438805, -0.0568747115119), (0.0109577355846, -0.0569686012891, -0.998315835043)
Vector: -0.263904928449, -6.1238575009, -32.3018729324)

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Components

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


Mass: 39383.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMBS, PBGD, UPS / Production host: Escherichia coli (E. coli) / References: UniProt: P08397, hydroxymethylbilane synthase
#2: Chemical ChemComp-7J8 / 3-[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]-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 838.810 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H46N4O16 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FWL / 3-[5-(aminomethyl)-4-(carboxymethyl)-2-iodo-1H-pyrrol-3-yl]propanoic acid / 2-iodoporphobilinogen


Mass: 352.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13IN2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: PEG 3350, diammonium hydrogen citrate, dithiothreitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.5 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.31→45.25 Å / Num. obs: 32296 / % possible obs: 97.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 45.61 Å2 / CC1/2: 0.994 / Rsym value: 0.084 / Net I/σ(I): 5.48
Reflection shellResolution: 2.31→2.45 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.46 / Num. unique obs: 9341 / CC1/2: 0.918 / Rsym value: 0.388 / % possible all: 94.2

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.18.2_3874refinement
XDSdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ECR

3ecr


Resolution: 2.31→45.25 Å / SU ML: 0.3174 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.402
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2765 1612 5 %
Rwork0.2272 30644 -
obs0.2296 32256 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.52 Å2
Refinement stepCycle: LAST / Resolution: 2.31→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4894 0 137 76 5107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00565121
X-RAY DIFFRACTIONf_angle_d1.01096955
X-RAY DIFFRACTIONf_chiral_restr0.0591796
X-RAY DIFFRACTIONf_plane_restr0.0088909
X-RAY DIFFRACTIONf_dihedral_angle_d21.95651900
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.958918539558 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.380.44811240.37022367X-RAY DIFFRACTION95.11
2.38-2.450.4591340.34562544X-RAY DIFFRACTION99.74
2.45-2.540.43451320.34362517X-RAY DIFFRACTION99.77
2.54-2.640.34461340.32012542X-RAY DIFFRACTION99.89
2.64-2.760.37781330.29232527X-RAY DIFFRACTION99.85
2.76-2.910.31991340.27692550X-RAY DIFFRACTION99.96
2.91-3.090.26531340.25222554X-RAY DIFFRACTION99.93
3.09-3.330.30371350.24472549X-RAY DIFFRACTION100
3.33-3.660.30651350.21612563X-RAY DIFFRACTION99.82
3.67-4.190.2491350.19372571X-RAY DIFFRACTION99.85
4.19-5.280.21021380.1712628X-RAY DIFFRACTION99.89
5.29-45.250.21021440.19232732X-RAY DIFFRACTION99.83
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)
11.502638168110.132508352076-2.435675396514.56300488996-1.546693673186.54555254854-0.159200366875-0.250621753043-0.3523112688360.1144992455540.04277278502440.1067304456320.81374054413-0.1771926335720.09594503708260.3143874867360.0437029683470.01115469295770.365902198710.04307476386380.3421953141062.5078887794928.53234618591.30626824914
25.04598137960.1593617536711.772367876270.4362139674370.7287282566196.142565848520.01087776308790.483120974197-0.126983169515-0.0643595920125-0.03279089372140.04991316285310.0299316914407-0.2152198435740.00252981292670.265960798043-0.004836982489660.05340780729390.2366739236440.008039571047710.291851919277-14.444887309433.3460238945-13.6873861346
36.49496434813-0.7628937866430.8978307279641.687052326880.5721477278312.907101053690.0402061053941-0.176926793550.6736016936240.0990294343749-0.0607756600267-0.0410502821815-0.1410280954590.1155856490570.05950989652230.254856911237-0.06066967365550.01043249214760.238470422762-0.06835261164520.248062095828-10.627759354239.59586958744.26184439322
46.423857592842.079959954661.753323888468.003753526183.80208697596.63310780521-0.2944489274180.1949142270590.3399652829930.01130389026380.04659937330170.306728457104-0.237208156976-0.318297273730.1835192226220.2113043540330.03166500980020.04445424673910.4018053024530.002261465936490.2401272585-24.897331504643.3865927663-0.858254270385
59.557135746031.976773515261.943877519963.744063905531.087391802135.47173888415-0.131625708636-0.7309875457760.1816122218870.04765773217440.0660442607961-0.2387829709230.1360114421690.04437283982110.01771487199440.2900478468040.07901408032120.07483111009490.3684367047420.01297015100570.173374861499-18.448982470841.20423190979.93588766749
64.708144139410.714391507449-1.009923318254.186102493421.879507090263.03666793146-0.2568869540210.238615033482-0.842936217177-0.0051218440651-0.1154261523410.06374182932380.491668472233-0.1398552551610.3004089753030.369950840946-0.08082903460070.08140964903250.4149558223490.02449748057360.422521041526-2.0879767286922.3325107008-35.9859878192
73.248512191330.1166421812960.8253294031941.29234969501-0.09295231396875.98317936664-0.0996290703909-0.412177239985-0.1938819007960.2390794327240.00583771189038-0.2308030005540.1682617079470.4321127822020.08711038949650.2797787599630.05856419039020.02878778571190.4535735429860.09295952048280.37513024867315.351936032129.1861976554-21.1938113693
87.079005903032.672162063081.01369523281.992024581620.1830205881254.15650865179-0.02944660107410.1260224838210.210683265819-0.0374024436457-0.03279666454240.047366599727-0.2302856227780.2278552314390.0664313024180.2691531411960.03859674816440.03392832987780.4306193414040.1495811605180.27122509735814.954888729335.2986144615-39.1382740835
95.376595427870.3669926327690.2588922344513.89786575623-1.191393421684.51082073673-0.1864041674680.3490657920780.0350723849856-0.07697032642680.09471659727310.0431827853247-0.1191328563960.1659240606360.0664345431660.2426915669940.001129793619760.0998360153350.4331458338220.01170461258320.28332031894720.506605836635.2175450375-42.4921780973
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 86 )AA19 - 861 - 51
22chain 'A' and (resid 87 through 206 )AA87 - 20652 - 171
33chain 'A' and (resid 207 through 257 )AA207 - 257172 - 222
44chain 'A' and (resid 258 through 298 )AA258 - 298223 - 263
55chain 'A' and (resid 299 through 358 )AA299 - 358264 - 323
66chain 'B' and (resid 19 through 99 )BB19 - 991 - 62
77chain 'B' and (resid 100 through 228 )BB100 - 22863 - 191
88chain 'B' and (resid 229 through 283 )BB229 - 283192 - 246
99chain 'B' and (resid 284 through 357 )BB284 - 357247 - 320

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