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- PDB-7ccx: Crystal structure of the holo form of human hydroxymethylbilane s... -

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Basic information

Entry
Database: PDB / ID: 7ccx
TitleCrystal structure of the holo form of human hydroxymethylbilane synthase
ComponentsPorphobilinogen deaminase
KeywordsTRANSFERASE / Porphyrin synthesis
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-DPM / Porphobilinogen deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,6074
Polymers78,7662
Non-polymers8412
Water2,864159
1
A: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8032
Polymers39,3831
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8032
Polymers39,3831
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.411, 80.815, 109.194
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

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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-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.: 2 / Source method: obtained synthetically / Formula: C20H24N2O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 1.97 Å3/Da / Density % sol: 37.63 %
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: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.84→43.15 Å / Num. obs: 53490 / % possible obs: 98.2 % / Redundancy: 4 % / Biso Wilson estimate: 29.86 Å2 / CC1/2: 0.997 / Rsym value: 0.07 / Net I/σ(I): 10.73
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.31 / Num. unique obs: 15522 / CC1/2: 0.915 / Rsym value: 0.452 / % possible all: 92

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.14_3260refinement
XDSdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ECR

3ecr


Resolution: 1.84→43.15 Å / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.1717 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1994 3.74 %Random selection
Rwork0.1942 51350 --
obs0.1961 53344 97.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.75 Å2
Refinement stepCycle: LAST / Resolution: 1.84→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 60 159 4939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064894
X-RAY DIFFRACTIONf_angle_d0.74526644
X-RAY DIFFRACTIONf_chiral_restr0.0514782
X-RAY DIFFRACTIONf_plane_restr0.0053861
X-RAY DIFFRACTIONf_dihedral_angle_d5.10543516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.890.33051250.31213232X-RAY DIFFRACTION87.1
1.89-1.940.37171380.29413543X-RAY DIFFRACTION95.51
1.94-20.31691420.26023653X-RAY DIFFRACTION99.16
2-2.060.30381450.24353721X-RAY DIFFRACTION99.61
2.06-2.130.29061430.22433692X-RAY DIFFRACTION99.46
2.13-2.220.3071420.21113679X-RAY DIFFRACTION99.22
2.22-2.320.27161430.22533686X-RAY DIFFRACTION98.41
2.32-2.440.27321430.20693666X-RAY DIFFRACTION98.32
2.44-2.590.30221410.20983655X-RAY DIFFRACTION97.58
2.59-2.80.30161430.21253673X-RAY DIFFRACTION97.75
2.8-3.080.26341440.21193695X-RAY DIFFRACTION98.54
3.08-3.520.28171470.18293791X-RAY DIFFRACTION99.6
3.52-4.440.18761480.15843803X-RAY DIFFRACTION99.55
4.44-43.150.18881500.16843861X-RAY DIFFRACTION96.53
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)
12.77787017635-0.622665264866-0.3261255295093.06916413799-0.2512890973782.114417452880.1459746204680.0810341797592-0.198824258607-0.244685581977-0.0698664420385-0.1968401645260.3905563725890.132187170349-0.08771878658590.4158719203340.0223004146623-0.04535510223510.343499822258-0.006207828913290.278388494631-6.24256171879-23.0159466307-28.6306414836
20.495083596376-0.08335650964180.1348191698963.339621769241.269266105455.6784090625-0.0401366729038-0.0380685786010.07063838403080.1169427183980.03341272120710.0377365517734-0.1756130123240.0738719800023-0.001110002596680.2115780190570.00594683963769-0.007085469814110.3009016920720.02593538830050.300885813588-12.4755601582-5.07405582702-13.3737752842
31.05747702858-1.09179317891-0.2421160367116.509590906350.7128257643122.165035714090.1091429517350.0980738433797-0.0334640306799-0.198732972301-0.08285662141750.1115150512910.112043732137-0.0757792007645-0.03336792109740.270007996166-0.0173351322204-0.05113619041540.2911118111850.03312543734930.202684597126-20.0062536146-3.04872412625-33.2755549214
45.394972820611.273100568641.458522502887.505132943792.322600590157.51433421767-0.13101356468-0.0462730279104-0.1084782163950.01570400103280.232844834841-0.725862560769-0.2256260376440.688438210445-0.09018408485340.200271860867-0.0297270326313-0.02975257359430.3307371447760.04089109575210.327086097563-37.4330945285-25.5758868697-5.93712471669
59.103298670675.967581744531.38018700276.8369995101-0.9654188153983.389673535660.0622407276303-0.308656240702-0.0356012372967-0.346856001418-0.261998198153-0.622326061439-0.1960066160340.3058605912420.1600212724990.3401201027280.05337249105930.0605109351940.374514817996-0.0590965413730.396258870861-31.8581908509-23.2876662069-10.8971125998
62.99017783647-2.6613669586-1.137429386137.137229071222.264864318544.5425779261-0.1454282117280.03608800469260.158112573315-0.4271801340140.35460122814-0.426629259369-0.1398733081250.375689396845-0.2064311705260.318509379815-0.0795106714779-0.04475399058820.3325163028960.01479030938530.32963441808-38.4786638332-14.0810405896-11.1636347532
75.771339012571.25096769625-0.5475959613114.183012742350.2920003956847.6963625631-0.182990185586-0.5151047082960.437723039791.20982157073-0.05418939131440.451080937457-0.2885860314140.263226340740.2277339221380.765498512540.02020194664420.004601781066170.336666069988-0.03770514362270.398664065283-45.31680560111.5053950966212.3140183736
87.49255574935-2.47023860112-0.9025383441579.016235345242.231046155825.57335508432-0.0744911738157-0.7825776152980.309122524951.136438008920.652415753411-1.23630691949-0.1935037070540.546166115136-0.5421510002180.7053657418770.0376729856258-0.1684099959380.532268282717-0.1354799919720.537663694093-37.8608826678-2.0432401306714.2295332948
94.52313669163-2.80174449313-0.5626000733452.303861778192.128220106225.91809959603-0.216428748593-0.2717739256610.01206197081310.66672499849-0.07075023599350.690184166090.0450011725589-0.1852274712140.2488564910250.433806519318-0.04061509534170.008699756454880.312067194054-0.01754570229350.345796654047-46.2752870298-10.9470464268.66666007411
101.66261437764-1.462505608770.2377023346747.233340688121.520853406551.30601813262-0.1299111722450.1255808513970.0267559498375-0.4014813683070.03155698432550.296065834073-0.2532224705420.03810637548970.1156239206660.309024336013-0.0465276183122-0.08740669053260.308775964540.04844935450780.298365044711-45.3002038454-10.5924954525-12.1819202083
116.110730853321.803960602352.993002627156.642314492311.610415214045.76894535467-0.1576509848820.1235811898840.352190970757-0.29612495468-0.08312343553990.510216746065-0.540089012706-0.1232007475640.2725954802470.4274579621130.0219550499359-0.05136057876880.2873334040630.05822216013340.357981388617-49.59205282373.80682342534-7.89578763231
121.123265678080.7998647414550.2289188918775.991419859653.320710931554.10913103254-0.0782451103099-0.003011665877130.20664538561-0.640964497787-0.08825474169680.0205354261402-0.4857021723520.1499495237690.1446183640930.490719964953-0.0346182909875-0.1401819103250.3755116891730.1047877592950.40178256455-45.45503268590.521367367564-16.8692021147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 228 )
3X-RAY DIFFRACTION3chain 'A' and (resid 229 through 354 )
4X-RAY DIFFRACTION4chain 'C' and (resid 18 through 45 )
5X-RAY DIFFRACTION5chain 'C' and (resid 46 through 86 )
6X-RAY DIFFRACTION6chain 'C' and (resid 87 through 120 )
7X-RAY DIFFRACTION7chain 'C' and (resid 121 through 157 )
8X-RAY DIFFRACTION8chain 'C' and (resid 158 through 184 )
9X-RAY DIFFRACTION9chain 'C' and (resid 185 through 206 )
10X-RAY DIFFRACTION10chain 'C' and (resid 207 through 256 )
11X-RAY DIFFRACTION11chain 'C' and (resid 257 through 298 )
12X-RAY DIFFRACTION12chain 'C' and (resid 299 through 357 )

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