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- PDB-1ll1: HYDROXO BRIDGE MET FORM HEMOCYANIN FROM LIMULUS -

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Basic information

Entry
Database: PDB / ID: 1ll1
TitleHYDROXO BRIDGE MET FORM HEMOCYANIN FROM LIMULUS
ComponentsMETCYANIN II
KeywordsOXYGEN TRANSPORT / RESPIRATORY PROTEIN / GLYCOPROTEIN
Function / homology
Function and homology information


chloride ion binding / oxygen transport / oxygen carrier activity / oxidoreductase activity / copper ion binding / extracellular region
Similarity search - Function
Hemocyanin, N-terminal domain / Hemocyanin, C-terminal domain / Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin, C-terminal domain superfamily / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal ...Hemocyanin, N-terminal domain / Hemocyanin, C-terminal domain / Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin, C-terminal domain superfamily / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain / Hemocyanin/hexamerin / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Hemocyanin, N-terminal domain / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Immunoglobulin E-set / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / Hemocyanin II
Similarity search - Component
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLiu, S. / Magnus, K.
CitationJournal: To be Published
Title: Crystallographic Studies of Hydroxo, Nitrosyl, Azido and Fluro met Form Hemocyanin Subunit II from Limulus
Authors: Liu, S. / Ton-that, H. / Magnus, K.
History
DepositionMar 17, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METCYANIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9064
Polymers72,7441
Non-polymers1633
Water2,468137
1
A: METCYANIN II
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)437,43724
Polymers436,4626
Non-polymers97518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Unit cell
Length a, b, c (Å)116.610, 116.610, 285.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein METCYANIN II / BIS(M-HYDROXO) MET FORM METCYANIN


Mass: 72743.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM HEMOLYMPH
Source: (natural) Limulus polyphemus (Atlantic horseshoe crab)
References: UniProt: P04253
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 51.9 % / Description: THREE DATA SETS MERGED
Crystal growpH: 6.8
Details: PROTEIN WAS CRYSTALLIZED FROM 4-6% PEG 3350, 0.2M BIS-TRIS, 0.5M NACL, 5MM H2O2. PH IN THE DROP NEAR 6.8.

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→58.3 Å / Num. obs: 22669 / % possible obs: 87.6 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 7.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.188 / % possible all: 39.4

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Processing

Software
NameVersionClassification
UCSDdata collection
SCALAIN CCP4data scaling
X-PLOR3.851model building
X-PLOR3.851refinement
UCSDdata reduction
CCP4(SCALA)data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LLA

1lla


Resolution: 2.55→60 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: THERE ARE SEVERAL RESIDUE
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2276 10 %RANDOM
Rwork0.167 ---
obs0.167 21960 88.6 %-
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1-17.434 Å27.064 Å20 Å2
2--17.434 Å20 Å2
3---17.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.55→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4763 0 4 135 4902
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.761.5
X-RAY DIFFRACTIONx_mcangle_it4.2422
X-RAY DIFFRACTIONx_scbond_it4.2972
X-RAY DIFFRACTIONx_scangle_it6.1952.5
LS refinement shellResolution: 2.55→2.67 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.279 156 11.1 %
Rwork0.248 1241 -
obs--45.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2

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