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- PDB-9kzl: Crystal structure of the functional unit (HtH1-h) of hemocyanin f... -

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Basic information

Entry
Database: PDB / ID: 9kzl
TitleCrystal structure of the functional unit (HtH1-h) of hemocyanin from Haliotis discus hannai,Containing a met site
Components(Hemocyanin type ...) x 2
KeywordsMETAL BINDING PROTEIN / Orbicular / copper coordination / Met state
Function / homology
Function and homology information


oxygen carrier activity / oxidoreductase activity / metal ion binding
Similarity search - Function
Haemocyanin beta-sandwich domain / Haemocyanin C-terminal domain superfamily / Haemocyanin beta-sandwich / Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily
Similarity search - Domain/homology
COPPER (II) ION / ETHANOL / alpha-D-mannopyranose / OXYGEN ATOM / HYDROXIDE ION / Hemocyanin type 1
Similarity search - Component
Biological speciesHaliotis discus hannai (Japanese disc abalone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhao, G.H. / Yang, H.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2021YDF2100105 China
CitationJournal: To Be Published
Title: Crystal structure of the functional unit (HtH1-h) of hemocyanin from Haliotis discus hannai,Containing a met state
Authors: Zhao, G.H. / Yang, H.C.
History
DepositionDec 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemocyanin type 1
B: Hemocyanin type 1
C: Hemocyanin type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,05719
Polymers169,9313
Non-polymers1,12616
Water19,8711103
1
A: Hemocyanin type 1
hetero molecules

A: Hemocyanin type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,04712
Polymers113,3062
Non-polymers74110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area4330 Å2
ΔGint-85 kcal/mol
Surface area36970 Å2
MethodPISA
2
B: Hemocyanin type 1
C: Hemocyanin type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,03413
Polymers113,2782
Non-polymers75611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-80 kcal/mol
Surface area37010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.573, 117.675, 97.588
Angle α, β, γ (deg.)90.000, 96.635, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Hemocyanin type ... , 2 types, 3 molecules ABC

#1: Protein Hemocyanin type 1 / Hemocyanin functional unit (HtH1-h)


Mass: 56653.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haliotis discus hannai (Japanese disc abalone)
References: UniProt: A0A7R6RYX0
#2: Protein Hemocyanin type 1 / Hemocyanin functional unit (HtH1-h)


Mass: 56639.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Haliotis discus hannai (Japanese disc abalone)
References: UniProt: A0A7R6RYX0

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Sugars , 1 types, 3 molecules

#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1116 molecules

#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1103 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: PEG 1000,Ethanol,Phosphate

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Data collection

DiffractionMean temperature: 283 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.999→28.6 Å / Num. obs: 126200 / % possible obs: 98.86 % / Redundancy: 3.5 % / Biso Wilson estimate: 26.01 Å2 / CC1/2: 0.98 / Net I/σ(I): 4.3
Reflection shellResolution: 2→2.02 Å / Mean I/σ(I) obs: 14.9 / Num. unique obs: 3720 / CC1/2: 0.988 / % possible all: 92.58

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-30007.21data reduction
HKL-30007.21data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QJO

3qjo


Resolution: 2→28.6 Å / SU ML: 0.1961 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2089 6302 4.99 %
Rwork0.1669 119896 -
obs0.169 126198 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.14 Å2
Refinement stepCycle: LAST / Resolution: 2→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11922 0 55 1103 13080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007112311
X-RAY DIFFRACTIONf_angle_d0.876416699
X-RAY DIFFRACTIONf_chiral_restr0.05531764
X-RAY DIFFRACTIONf_plane_restr0.00772155
X-RAY DIFFRACTIONf_dihedral_angle_d15.81274454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.26251980.2053720X-RAY DIFFRACTION92.58
2.02-2.050.24592060.19363938X-RAY DIFFRACTION97.64
2.05-2.070.23182260.18933897X-RAY DIFFRACTION97.7
2.07-2.10.25162020.18733996X-RAY DIFFRACTION98.11
2.1-2.120.21862130.18063921X-RAY DIFFRACTION97.99
2.12-2.150.24512110.17973915X-RAY DIFFRACTION98.12
2.15-2.180.25092030.1844011X-RAY DIFFRACTION98.02
2.18-2.220.21022030.18483955X-RAY DIFFRACTION98.34
2.22-2.250.24482010.18243996X-RAY DIFFRACTION98.82
2.25-2.290.22852140.17543943X-RAY DIFFRACTION98.69
2.29-2.330.23721780.18423999X-RAY DIFFRACTION98.72
2.33-2.370.23641980.17873986X-RAY DIFFRACTION98.8
2.37-2.420.22512100.18133994X-RAY DIFFRACTION98.85
2.42-2.460.22412090.18633999X-RAY DIFFRACTION99.22
2.46-2.520.23832310.18574021X-RAY DIFFRACTION99.35
2.52-2.580.23452400.17363948X-RAY DIFFRACTION99.08
2.58-2.640.2282120.17564062X-RAY DIFFRACTION99.42
2.64-2.710.21072130.17743996X-RAY DIFFRACTION99.43
2.71-2.790.22812030.1834020X-RAY DIFFRACTION99.51
2.79-2.880.23311990.17624007X-RAY DIFFRACTION99.64
2.88-2.980.23832620.17473957X-RAY DIFFRACTION99.62
2.99-3.10.21832400.1724047X-RAY DIFFRACTION99.88
3.1-3.250.21141940.17244059X-RAY DIFFRACTION99.88
3.25-3.420.20271900.15994074X-RAY DIFFRACTION99.93
3.42-3.630.18112050.15764046X-RAY DIFFRACTION99.86
3.63-3.910.19982070.15314061X-RAY DIFFRACTION99.93
3.91-4.30.17421890.13964081X-RAY DIFFRACTION99.95
4.3-4.920.17012130.14074068X-RAY DIFFRACTION99.88
4.92-6.190.19222060.16144086X-RAY DIFFRACTION99.98
6.19-28.60.1812260.1614093X-RAY DIFFRACTION98.92

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