1fzf

CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN WITH THE PEPTIDE LIGAND GLY-HIS-ARG-PRO-AMIDE

Method: X-RAY DIFFRACTION D_max: 211.4 Å Quality: REASONABLE

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	1fzf
沉积日期 deposition_date	1998-12-28
结构标题 title	CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN WITH THE PEPTIDE LIGAND GLY-HIS-ARG-PRO-AMIDE
关键词 keywords	BLOOD COAGULATION, PLASMA, PLATELET, FIBRINOGEN, FIBRIN; BLOOD COAGULATION
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	54.03 Å
回转半径 Rg (电子) rg_electron	55.54 Å
零角强度 I(0) i0	358267000.00
分子量 molecular_weight	150610.0 kDa
排除体积 excluded_volume	185890 Å³
包络体积 envelope_volume	248280 Å³
水化壳体积 shell_volume	44949 Å³
包络直径 envelope_diameter	221.8 Å
壳层 Rg shell_rg	43.55 Å
包络 Rg envelope_rg	56.90 Å
形状 Rg shape_rg	55.43 Å
总 Rg total_rg	55.48 Å
总原子数 total_atoms	10581
残基数 n_residues	1313
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	211.4 Å
Rg (实空间) rg_real	55.12 Å
Rg 误差 (实空间) rg_real_error	4.51 Å
I(0) (实空间) i0_real	3.5830e+08
I(0) 误差 (实空间) i0_real_error	8.9480e+06
Rg (倒空间) rg_reciprocal	53.12 Å
I(0) (倒空间) i0_reciprocal	357200000.0000
解质量估计 total_estimate	0.5868
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	29.2 Å
偏度 Skewness skewness	0.718
峰度 Kurtosis kurtosis	-0.199
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11680000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.170; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.119; Smooth: 0.000

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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 (6)

Entity 1 polymer

描述 description	FIBRINOGEN
分子量 formula_weight	10245.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D
原子数 atom_count	10581

VSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRALAREVDLKDYEDQQKQLEQVIAKDLLPSR

Entity 2 polymer

描述 description	FIBRINOGEN
分子量 formula_weight	37692.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,E

DNENVVNEYSSELEKHQLYIDETVNSNIPTNLRVLRSILENLRSKIQKLESDVSAQMEYCRTPCTVSCNIPVVSGKECEEIIRKGGETSEMYLIQPDSSVKPYRVYCDMNTENGGWTVIQNRQDGSVDFGRKWDPYKQGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRMGPTELLIEMEDWKGDKVKAHYGGFTVQNEANKYQISVNKYRGTAGNALMDGASQLMGENRTMTIHNGMFFSTYDRDNDGWLTSDPRKQCSKEDGGGWWYNRCHAANPNGRYYWGGQYTWDMAKHGTDDGVVWMNWKGSWYSMRKMSMKIRPFFPQQ

Entity 3 polymer

描述 description	FIBRINOGEN
分子量 formula_weight	36223.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,F

KMLEEIMKYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHDITGKDCQDIANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKRLDGSVDFKKNWIQYKEGFGHLSPTGTTEFWLGNEKIHLISTQSAIPYALRVELEDWNGRTSTADYAMFKVGPEADKYRLTYAYFAGGDAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNCAEQDGSGWWMNKCHAGHLNGVYYQGGTYSKASTPNGYDNGIIWATWKTRWYSMKKTTMKIIPFNRLTIGEGQQHHLGGAK

Entity 4 polymer

描述 description	FIBRINOGEN
分子量 formula_weight	467.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	S,T,M,N

GHRP

Entity 5 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1fzfa_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
家族 Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

结构域编号 domain_id	d1fzfb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
家族 Family family	d.171.1.1 — Fibrinogen C-terminal domain-like

结构域编号 domain_id	d1fzfb2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
家族 Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

结构域编号 domain_id	d1fzfc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
家族 Family family	d.171.1.1 — Fibrinogen C-terminal domain-like

结构域编号 domain_id	d1fzfc2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
家族 Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

结构域编号 domain_id	d1fzfd_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
家族 Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

结构域编号 domain_id	d1fzfe1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
家族 Family family	d.171.1.1 — Fibrinogen C-terminal domain-like

结构域编号 domain_id	d1fzfe2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
家族 Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

结构域编号 domain_id	d1fzff1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
家族 Family family	d.171.1.1 — Fibrinogen C-terminal domain-like

结构域编号 domain_id	d1fzff2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
家族 Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

CATH v4.4 (10 domains)

结构域编号 domain_id	1fzfA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1fzfB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

结构域编号 domain_id	1fzfB02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

结构域编号 domain_id	1fzfC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

结构域编号 domain_id	1fzfC02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

结构域编号 domain_id	1fzfD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1fzfE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

结构域编号 domain_id	1fzfE02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

结构域编号 domain_id	1fzfF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

结构域编号 domain_id	1fzfF02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	54.800 Å
晶胞边长 b length_b	149.400 Å
晶胞边长 c length_c	234.700 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.3020

fit	/app/data/saxs_computation/fz/1fzf/1fzf.fit
pddf	/app/data/pr_computation/fz/1fzf/1fzf.pr.out
profile	/app/data/saxs_computation/fz/1fzf/1fzf.dat

CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN WITH THE PEPTIDE LIGAND GLY-HIS-ARG-PRO-AMIDE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

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

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

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)