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- PDB-4zel: Human dopamine beta-hydroxylase -

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Basic information

Entry
Database: PDB / ID: 4zel
TitleHuman dopamine beta-hydroxylase
ComponentsDopamine beta-hydroxylase
KeywordsOXIDOREDUCTASE / hydroxylase / dimer / copper binding
Function / homology
Function and homology information


dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / octopamine biosynthetic process / cytokine production / homoiothermy / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen / chromaffin granule lumen / regulation of extrinsic apoptotic signaling pathway / norepinephrine biosynthetic process ...dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / octopamine biosynthetic process / cytokine production / homoiothermy / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen / chromaffin granule lumen / regulation of extrinsic apoptotic signaling pathway / norepinephrine biosynthetic process / Catecholamine biosynthesis / catecholamine biosynthetic process / chromaffin granule membrane / behavioral response to ethanol / maternal behavior / dopamine catabolic process / fear response / L-ascorbic acid binding / response to pain / transport vesicle membrane / leukocyte migration / centriolar satellite / blood vessel remodeling / catalytic activity / positive regulation of vasoconstriction / response to amphetamine / secretory granule membrane / locomotory behavior / visual learning / memory / glucose homeostasis / positive regulation of cold-induced thermogenesis / regulation of cell population proliferation / chemical synaptic transmission / secretory granule lumen / membrane => GO:0016020 / copper ion binding / intracellular membrane-bounded organelle / synapse / endoplasmic reticulum / extracellular space / extracellular region / membrane / cytoplasm
Similarity search - Function
DOMON domain / Dopamine beta-hydroxylase-like / Tyramine beta-hydroxylase/Dopamine beta-hydroxylase / DOMON domain profile. / DOMON domain / Possible catecholamine-binding domain present in a variety of eukaryotic proteins. / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / Copper type II, ascorbate-dependent monooxygenase, N-terminal / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site ...DOMON domain / Dopamine beta-hydroxylase-like / Tyramine beta-hydroxylase/Dopamine beta-hydroxylase / DOMON domain profile. / DOMON domain / Possible catecholamine-binding domain present in a variety of eukaryotic proteins. / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / Copper type II, ascorbate-dependent monooxygenase, N-terminal / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site / Copper type II ascorbate-dependent monooxygenase, C-terminal / Copper type II, ascorbate-dependent monooxygenase, N-terminal domain superfamily / Copper type II ascorbate-dependent monooxygenase, N-terminal domain / Copper type II ascorbate-dependent monooxygenase, C-terminal domain / Copper type II, ascorbate-dependent monooxygenases signature 1. / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal
Similarity search - Domain/homology
COPPER (II) ION / Dopamine beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsVendelboe, T.V. / Harris, P. / Christensen, H.E.M. / Harlos, K. / Walter, T. / Zhao, Y. / Omari, K.
CitationJournal: Sci Adv / Year: 2016
Title: The crystal structure of human dopamine beta-hydroxylase at 2.9 angstrom resolution.
Authors: Vendelboe, T.V. / Harris, P. / Zhao, Y. / Walter, T.S. / Harlos, K. / El Omari, K. / Christensen, H.E.
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dopamine beta-hydroxylase
B: Dopamine beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,8849
Polymers130,0322
Non-polymers2,8527
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint1 kcal/mol
Surface area50730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.810, 119.060, 224.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dopamine beta-hydroxylase / / Dopamine beta-monooxygenase


Mass: 65015.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DBH / Organ: KIDNEY / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P09172, dopamine beta-monooxygenase

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Sugars , 4 types, 6 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 13 molecules

#5: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 12% PEG3350, 0.2 M potassium nitrate / PH range: 4.2-4.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0073 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0073 Å / Relative weight: 1
ReflectionResolution: 2.9→63.98 Å / Num. obs: 30957 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.068 / Net I/σ(I): 10.6 / Num. measured all: 202337
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
2.9-2.986.91.2631.61539622310.56199.8
12.97-63.985.30.03134.420613890.01697.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
xia20.3.5.0data reduction
PDB_EXTRACT3.15data extraction
xia2data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→59.53 Å / FOM work R set: 0.7596 / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2696 1560 5.05 %
Rwork0.2295 29356 -
obs0.2315 30916 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.03 Å2 / Biso mean: 75.18 Å2 / Biso min: 29.48 Å2
Refinement stepCycle: final / Resolution: 2.9→59.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8716 0 185 12 8913
Biso mean--102.34 41.88 -
Num. residues----1094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079193
X-RAY DIFFRACTIONf_angle_d1.45712514
X-RAY DIFFRACTIONf_chiral_restr0.061402
X-RAY DIFFRACTIONf_plane_restr0.0061604
X-RAY DIFFRACTIONf_dihedral_angle_d15.5053386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.99360.34531230.334226262749100
2.9936-3.10060.36331390.321726392778100
3.1006-3.22480.3261600.291826142774100
3.2248-3.37150.29561410.284426252766100
3.3715-3.54930.31141510.260826592810100
3.5493-3.77160.28641420.247726602802100
3.7716-4.06270.3071500.229626232773100
4.0627-4.47150.25081430.208926852828100
4.4715-5.11820.22151280.186426912819100
5.1182-6.44720.25281630.209627062869100
6.4472-59.54250.21991200.20042828294899
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)
15.9964.1764-5.44713.8439-5.38328.03350.45580.05710.70340.9320.40330.4014-0.8818-0.3585-0.79180.65660.076-0.02050.60840.04140.7633.496932.609237.0037
26.187-0.6792-0.48045.50890.13446.75250.06190.61880.2807-0.93640.14830.7592-0.1423-0.7664-0.19940.6565-0.0485-0.14780.55810.04820.67311.208729.234623.9044
32.38540.84041.99021.2114-0.38234.0880.0305-0.42960.24010.3845-0.1059-0.5588-0.44420.89930.18280.84310.12340.02750.96370.02390.868925.970627.974444.6955
44.4326-0.3475-0.64554.7524-1.20422.44140.12280.28940.06060.199-0.342-0.85840.11861.4740.27390.85110.0064-0.14781.35470.03570.939932.177523.639652.8219
52.4868-0.7323-0.61243.10021.60764.42890.0366-0.20580.02570.15590.0865-0.1317-0.00520.1403-0.06340.4451-0.0144-0.06970.44050.07940.518420.50976.250942.9235
63.72840.8521-1.16973.23222.84229.1446-0.0757-0.1487-0.2520.11030.2378-0.45270.81880.412-0.27610.67020.0765-0.04160.50680.15750.565329.8941-5.307736.8513
70.118-0.46730.35883.584-2.79742.1625-0.5757-0.6246-0.35550.63250.85860.4733-0.3385-0.7473-0.29440.886-0.0361-0.15550.84360.0460.57889.18152.853541.6881
85.67140.5854-0.06284.92140.33625.56090.1628-0.47390.5029-0.0597-0.20270.3581-0.53940.00430.05150.6861-0.0476-0.07610.5497-0.10640.5058-23.8274-3.328.5738
94.59351.30160.21150.9838-0.02860.7143-0.2410.7145-0.3592-0.20410.2733-0.06670.1936-0.0454-0.06920.7145-0.03030.00510.523-0.05030.4869-8.1977-20.371910.6285
104.58380.1736-1.2341.46840.98853.0938-0.14220.398-0.2448-0.2034-0.2272-0.20390.10580.43010.17910.6498-0.0304-0.05120.385-0.05630.647713.5035-15.359320.0811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 78 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 187 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 236 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 237 through 362 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 363 through 523 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 524 through 576 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 577 through 611 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 187 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 188 through 523 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 524 through 612 )B0

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