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- PDB-7ccy: Crystal structure of the 2-iodoporphobilinogen-bound holo form of... -

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Basic information

Entry
Database: PDB / ID: 7ccy
TitleCrystal structure of the 2-iodoporphobilinogen-bound holo form of human hydroxymethylbilane synthase
ComponentsPorphobilinogen deaminase
KeywordsTRANSFERASE / Porphyrin synthesis / Inhibitor
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-DPM / Chem-FWL / Porphobilinogen deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)79,9595
Polymers78,7662
Non-polymers1,1933
Water1,15364
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)40,1563
Polymers39,3831
Non-polymers7732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.011, 81.237, 109.097
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 21 or (resid 22...
21(chain "C" and (resid 19 through 31 or resid 33...
12(chain "A" and resid 401)
22(chain "C" and resid 401)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
111ARGALAA1 - 13
121ILELEUA17 - 221
131HISILEA225 - 268
141PROLYSA284 - 319
151ILEALAA323 - 327
211ARGALAB - C1 - 13
221ILELYSB - C15 - 44
231GLULEUB - C57 - 231
241HISILEB - C233 - 276
251PROLYSB - C278 - 313
261ILEALAB - C315 - 319
112DPMDPMD - A
212DPMDPME - C

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.999988225879, -0.0040129327523, -0.00272845648854), (0.00404750045885, 0.999910088221, 0.0127841000423), (0.00267690943439, -0.0127949929497, 0.999914557505)-31.8289356402, 0.55140361911, 18.5292900787
2given(0.999950392427, 0.00262908985947, -0.00960731862372), (-0.00194663261382, 0.997519317318, 0.0703663428015), (0.00976848535309, -0.0703441501783, 0.997474950678)-31.9369081803, 1.47106497999, 18.2003944871

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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: 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.: 64 / 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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: PEG 3350, diammonium hydrogen citrate, dithothreitol

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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: RAYONIX MX225HE / Detector: CCD / Date: Jul 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.4→48.91 Å / Num. obs: 25907 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.75 Å2 / CC1/2: 0.997 / Rsym value: 0.102 / Net I/σ(I): 11.3
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 7702 / CC1/2: 0.851 / Rsym value: 0.623 / % possible all: 95.8

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Processing

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

3ecr


Resolution: 2.4→48.91 Å / SU ML: 0.3202 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.7764
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1293 5 %Random selection
Rwork0.2017 24581 --
obs0.2053 25874 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.64 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 0 77 64 4963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00965013
X-RAY DIFFRACTIONf_angle_d1.31916812
X-RAY DIFFRACTIONf_chiral_restr0.067800
X-RAY DIFFRACTIONf_plane_restr0.008886
X-RAY DIFFRACTIONf_dihedral_angle_d20.90791843
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
12AX-RAY DIFFRACTIONTorsion NCS1.52839717372
22AX-RAY DIFFRACTIONTorsion NCS0.253287830809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50.37881380.29082599X-RAY DIFFRACTION95.23
2.5-2.610.36721390.27792658X-RAY DIFFRACTION97.12
2.61-2.750.33511420.26452699X-RAY DIFFRACTION98.03
2.75-2.920.29061400.2462673X-RAY DIFFRACTION97.78
2.92-3.150.33371430.23052708X-RAY DIFFRACTION98.41
3.15-3.460.32521430.2122730X-RAY DIFFRACTION98.97
3.46-3.960.23291440.18292756X-RAY DIFFRACTION99.11
3.96-4.990.19411490.1462824X-RAY DIFFRACTION99.7
4.99-48.910.2511550.17552934X-RAY DIFFRACTION99.77

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