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- PDB-1lnl: Structure of deoxygenated hemocyanin from Rapana thomasiana -

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Basic information

Entry
Database: PDB / ID: 1lnl
TitleStructure of deoxygenated hemocyanin from Rapana thomasiana
Componentshemocyanin
KeywordsOXYGEN STORAGE/TRANSPORT / hemocyanin / deoxygenated form / oxygen / metal binding site / cooperativity / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


oxygen carrier activity / oxidoreductase activity / extracellular space / metal ion binding
Similarity search - Function
Haemocyanin C-terminal domain / Hemocyanin; Chain: A, domain 2 / Haemocyanin beta-sandwich domain / Haemocyanin C-terminal domain superfamily / Haemocyanin beta-sandwich / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. ...Haemocyanin C-terminal domain / Hemocyanin; Chain: A, domain 2 / Haemocyanin beta-sandwich domain / Haemocyanin C-terminal domain superfamily / Haemocyanin beta-sandwich / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / 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 / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / Hemocyanin type 2 unit e
Similarity search - Component
Biological speciesRapana thomasiana (veined rapa whelk)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsPerbandt, M. / Guthoehrlein, E.W. / Rypniewski, W. / Idakieva, K. / Stoeva, S. / Voelter, W. / Genov, N. / Betzel, C.
CitationJournal: Biochemistry / Year: 2003
Title: The structure of a functional unit from the wall of a gastropod hemocyanin offers a possible mechanism for cooperativity
Authors: Perbandt, M. / Guthoehrlein, E.W. / Rypniewski, W. / Idakieva, K. / Stoeva, S. / Voelter, W. / Genov, N. / Betzel, C.
History
DepositionMay 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 4, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.4Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Revision 1.5Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 999 sequence Authors informed that protein sequence has not yet been deposited in a reference database. ... sequence Authors informed that protein sequence has not yet been deposited in a reference database. Sequence published by Stoeva et al., Arch. Biochem. Biophys. 339, 149-158 (2002). Authors also informed that they are unsure if a residue is present between ARG -1 and ASN 1 on chains A,B and C.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hemocyanin
B: hemocyanin
C: hemocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,60815
Polymers140,3723
Non-polymers1,23612
Water0
1
A: hemocyanin
B: hemocyanin
C: hemocyanin
hetero molecules

A: hemocyanin
B: hemocyanin
C: hemocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,21630
Polymers280,7456
Non-polymers2,47124
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Unit cell
Length a, b, c (Å)105.486, 105.486, 374.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: PRO / Refine code: 5 / Auth seq-ID: 15 - 350 / Label seq-ID: 18 - 353

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein hemocyanin /


Mass: 46790.805 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rapana thomasiana (veined rapa whelk) / References: UniProt: P83040
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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
#3: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu

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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: 3.71 Å3/Da / Density % sol: 66.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Mg formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop / Details: Perbandt, M., (2001) Acta Crystallogr., D57, 1663.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
20.2 Mmagnesium formate1reservoir
320 mMTris-HCl1reservoirpH7.8

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Data collection

DiffractionMean temperature: 243 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.921 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 20, 2000
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 33066 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.3→3.383 Å / % possible all: 99.1
Reflection
*PLUS
Highest resolution: 3.38 Å / % possible obs: 99.8 % / Num. measured all: 792618 / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
Highest resolution: 3.38 Å / Lowest resolution: 3.55 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→15 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.853 / SU ML: 0.224 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.8 / ESU R Free: 0.549 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28756 1653 5.1 %RANDOM
Rwork0.24776 ---
obs0.24974 30824 100 %-
all-33066 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.61 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 3.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9930 0 54 0 9984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0450.02110296
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.11.92314012
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9831218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.942151673
X-RAY DIFFRACTIONr_chiral_restr0.1740.21437
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028212
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3580.36599
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2550.5865
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.450.388
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.51
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A135tight positional0.280.05
2B135tight positional0.30.05
3C135tight positional0.360.05
1A1266medium positional0.480.5
2B1266medium positional0.540.5
3C1266medium positional0.620.5
1A1305loose positional1.075
2B1305loose positional1.035
3C1305loose positional1.185
LS refinement shellResolution: 3.3→3.382 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.388 122
Rwork0.296 2125
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)
11.5604-1.08180.44862.6479-1.16862.37450.10060.288-0.0405-0.4023-0.1323-0.10230.40510.06990.03170.30120.01290.01140.1858-0.00160.116577.857-8.3989239.2718
22.9210.9601-1.05711.6764-0.90052.58540.04320.29110.0874-0.06930.10940.0248-0.1339-0.25-0.15260.16740.06110.03570.04290.03990.042588.971233.4584263.6536
32.7757-1.2438-0.53462.55440.58872.62440.12750.3355-0.3611-0.305-0.15480.08860.04620.09850.02720.04280.0130.00770.31060.00440.1653129.200914.8898285.5671
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 4054 - 408
2X-RAY DIFFRACTION2BB1 - 4054 - 408
3X-RAY DIFFRACTION3CC1 - 4054 - 408
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.38 Å / Lowest resolution: 15 Å / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.04
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg3.1
LS refinement shell
*PLUS
Highest resolution: 3.38 Å / Lowest resolution: 3.55 Å

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