1hcy

CRYSTAL STRUCTURE OF HEXAMERIC HAEMOCYANIN FROM PANULIRUS INTERRUPTUS REFINED AT 3.2 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION D_max: 151.3 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hcy
沉积日期 deposition_date	1991-05-15
结构标题 title	CRYSTAL STRUCTURE OF HEXAMERIC HAEMOCYANIN FROM PANULIRUS INTERRUPTUS REFINED AT 3.2 ANGSTROMS RESOLUTION
关键词 keywords	OXYGEN TRANSPORT; OXYGEN TRANSPORT
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	48.79 Å
回转半径 Rg (电子) rg_electron	47.73 Å
零角强度 I(0) i0	2959890000.00
分子量 molecular_weight	447210.0 kDa
排除体积 excluded_volume	554810 Å³
包络体积 envelope_volume	728160 Å³
水化壳体积 shell_volume	119300 Å³
包络直径 envelope_diameter	149.0 Å
壳层 Rg shell_rg	57.65 Å
包络 Rg envelope_rg	46.75 Å
形状 Rg shape_rg	47.70 Å
总 Rg total_rg	48.13 Å
总原子数 total_atoms	31604
残基数 n_residues	3864
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	151.3 Å
Rg (实空间) rg_real	48.33 Å
Rg 误差 (实空间) rg_real_error	0.69 Å
I(0) (实空间) i0_real	2.9600e+09
I(0) 误差 (实空间) i0_real_error	4.3470e+07
Rg (倒空间) rg_reciprocal	48.79 Å
I(0) (倒空间) i0_reciprocal	2962000000.0000
解质量估计 total_estimate	0.8852
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	66.2 Å
偏度 Skewness skewness	0.036
峰度 Kurtosis kurtosis	-0.517
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	470400000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.919

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	ARTHROPODAN HEMOCYANIN
分子量 formula_weight	75696.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	31790

DALGTGNAQKQQDINHLLDKIYEPTKYPDLKDIAENFNPLGDTSIYNDHGAAVETLMKELNDHRLLEQRHWYSLFNTRQRKEALMLFAVLNQCKEWYCFRSNAAYFRERMNEGEFVYALYVSVIHSKLGDGIVLPPLYQITPHMFTNSEVIDKAYSAKMTQKPGTFNVSFTGTKKNREQRVAYFGEDIGMNIHHVTWHMDFPFWWEDSYGYHLDRKGELFFWVHHQLTARFDFERLSNWLDPVDELHWDRIIREGFAPLTSYKYGGEFPVRPDNIHFEDVDGVAHVHDLEITESRIHEAIDHGYITDSDGHTIDIRQPKGIELLGDIIESSKYSSNVQYYGSLHNTAHVMLGRQGDPHGKFNLPPGVMEHFETATRDPSFFRLHKYMDNIFKKHTDSFPPYTHDNLEFSGMVVNGVAIDGELITFFDEFQYSLINAVDSGENIEDVEINARVHRLNHNEFTYKITMSNNNDGERLATFRIFLCPIEDNNGITLTLDEARWFCIELDKFFQKVPSGPETIERSSKDSSVTVPDMPSFQSLKEQADNAVNGGHDLDLSAYERSCGIPDRMLLPKSKPEGMEFNLYVAVTDGDKDTEGHNGGHDYGGTHAQCGVHGEAYPDNRPLGYPLERRIPDERVIDGVSNIKHVVVKIVHHLEHHD

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	6

Entity 3 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	186

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6. 折叠分类 (SCOP + CATH) 30 domains

SCOP 2.08 (18 domains)

结构域编号 domain_id	d1hcya1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.85 — Hemocyanin, N-terminal domain
超家族 Superfamily superfamily	a.85.1 — Hemocyanin, N-terminal domain
家族 Family family	a.85.1.1 — Hemocyanin, N-terminal domain

结构域编号 domain_id	d1hcya2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.86 — Di-copper centre-containing domain
超家族 Superfamily superfamily	a.86.1 — Di-copper centre-containing domain
家族 Family family	a.86.1.1 — Hemocyanin middle domain

结构域编号 domain_id	d1hcya3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.3 — Arthropod hemocyanin, C-terminal domain

结构域编号 domain_id	d1hcyb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.85 — Hemocyanin, N-terminal domain
超家族 Superfamily superfamily	a.85.1 — Hemocyanin, N-terminal domain
家族 Family family	a.85.1.1 — Hemocyanin, N-terminal domain

结构域编号 domain_id	d1hcyb2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.86 — Di-copper centre-containing domain
超家族 Superfamily superfamily	a.86.1 — Di-copper centre-containing domain
家族 Family family	a.86.1.1 — Hemocyanin middle domain

结构域编号 domain_id	d1hcyb3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.3 — Arthropod hemocyanin, C-terminal domain

结构域编号 domain_id	d1hcyc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.85 — Hemocyanin, N-terminal domain
超家族 Superfamily superfamily	a.85.1 — Hemocyanin, N-terminal domain
家族 Family family	a.85.1.1 — Hemocyanin, N-terminal domain

结构域编号 domain_id	d1hcyc2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.86 — Di-copper centre-containing domain
超家族 Superfamily superfamily	a.86.1 — Di-copper centre-containing domain
家族 Family family	a.86.1.1 — Hemocyanin middle domain

结构域编号 domain_id	d1hcyc3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.3 — Arthropod hemocyanin, C-terminal domain

结构域编号 domain_id	d1hcyd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.85 — Hemocyanin, N-terminal domain
超家族 Superfamily superfamily	a.85.1 — Hemocyanin, N-terminal domain
家族 Family family	a.85.1.1 — Hemocyanin, N-terminal domain

结构域编号 domain_id	d1hcyd2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.86 — Di-copper centre-containing domain
超家族 Superfamily superfamily	a.86.1 — Di-copper centre-containing domain
家族 Family family	a.86.1.1 — Hemocyanin middle domain

结构域编号 domain_id	d1hcyd3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.3 — Arthropod hemocyanin, C-terminal domain

结构域编号 domain_id	d1hcye1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.85 — Hemocyanin, N-terminal domain
超家族 Superfamily superfamily	a.85.1 — Hemocyanin, N-terminal domain
家族 Family family	a.85.1.1 — Hemocyanin, N-terminal domain

结构域编号 domain_id	d1hcye2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.86 — Di-copper centre-containing domain
超家族 Superfamily superfamily	a.86.1 — Di-copper centre-containing domain
家族 Family family	a.86.1.1 — Hemocyanin middle domain

结构域编号 domain_id	d1hcye3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.3 — Arthropod hemocyanin, C-terminal domain

结构域编号 domain_id	d1hcyf1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.85 — Hemocyanin, N-terminal domain
超家族 Superfamily superfamily	a.85.1 — Hemocyanin, N-terminal domain
家族 Family family	a.85.1.1 — Hemocyanin, N-terminal domain

结构域编号 domain_id	d1hcyf2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.86 — Di-copper centre-containing domain
超家族 Superfamily superfamily	a.86.1 — Di-copper centre-containing domain
家族 Family family	a.86.1.1 — Hemocyanin middle domain

结构域编号 domain_id	d1hcyf3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.3 — Arthropod hemocyanin, C-terminal domain

CATH v4.4 (12 domains)

结构域编号 domain_id	1hcyA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1280 — di-copper center containing domain from catechol oxidase
同源超家族 H-superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

结构域编号 domain_id	1hcyA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1520 — Hemocyanin, C-terminal domain

结构域编号 domain_id	1hcyB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1280 — di-copper center containing domain from catechol oxidase
同源超家族 H-superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

结构域编号 domain_id	1hcyB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1520 — Hemocyanin, C-terminal domain

结构域编号 domain_id	1hcyC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1280 — di-copper center containing domain from catechol oxidase
同源超家族 H-superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

结构域编号 domain_id	1hcyC03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1520 — Hemocyanin, C-terminal domain

结构域编号 domain_id	1hcyD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1280 — di-copper center containing domain from catechol oxidase
同源超家族 H-superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

结构域编号 domain_id	1hcyD03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1520 — Hemocyanin, C-terminal domain

结构域编号 domain_id	1hcyE02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1280 — di-copper center containing domain from catechol oxidase
同源超家族 H-superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

结构域编号 domain_id	1hcyE03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1520 — Hemocyanin, C-terminal domain

结构域编号 domain_id	1hcyF02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1280 — di-copper center containing domain from catechol oxidase
同源超家族 H-superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

结构域编号 domain_id	1hcyF03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1520 — Hemocyanin, C-terminal domain

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7. 引用文献 (8)

Crystal structure of hexameric haemocyanin from Panulirus interruptus refined at 3.2 A resolution.

J.Mol.Biol. (1989)

PMID: 2585484 · DOI: 10.1016/0022-2836(89)90276-3 PRIMARY

Spectroscopic Investigations of Panulirus Interruptus Hemocyanin in the Crystalline State

Eur.J.Biochem. (1989)

;Pseudo 2-Fold Symmetry in the Copper-Binding Domain of Arthropodan Haemocyanins. Possible Implications for the Evolution of Oxygen Transport Proteins ;

J.Mol.Biol. (1989)

;Panulirus Interruptus Hemocyanin. The Amino Acid Sequence of Subunit B and Anomalous Behavior of Subunits a and B on Polyacrylamide Gel Electrophoresis in the Presence of /Sds ;

Eur.J.Biochem. (1988)

Panulirus Interruptus Hemocyanin. The Elucidation of the Complete Amino Acid Sequence of Subunit A

Eur.J.Biochem. (1987)

;Structure Determination of Panulirus Interruptus Haemocyanin at 3.2 Angstroms Resolution. Successful Phase Extension by Sixfold Density Averaging ;

J.Mol.Biol. (1986)

The Structure of Arthropod Hemocyanins

Science (1985)

3.2 Angstroms Structure of the Copper-Containing, Oxygen-Carrying Protein Panulirus Interruptus Haemocyanin

Nature (1984)

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晶胞边长 a length_a	119.800 Å
晶胞边长 b length_b	193.100 Å
晶胞边长 c length_c	122.200 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	118.10 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	3.200 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.2210
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/hc/1hcy/1hcy.fit
pddf	/app/data/pr_computation/hc/1hcy/1hcy.pr.out
profile	/app/data/saxs_computation/hc/1hcy/1hcy.dat