1o6z

;1.95 A resolution structure of (R207S,R292S) mutant of malate dehydrogenase from the halophilic archaeon Haloarcula marismortui (holo form) ;

Method: X-RAY DIFFRACTION D_max: 95.6 Å Quality: EXCELLENT

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	1o6z
沉积日期 deposition_date	2002-10-22
结构标题 title	;1.95 A resolution structure of (R207S,R292S) mutant of malate dehydrogenase from the halophilic archaeon Haloarcula marismortui (holo form) ;
关键词 keywords	HALOPHILIC, ION-BINDING, PROTEIN-SOLVENT INTERACTION, MALATE DEHYDROGENASE, OXIDOREDUCTASE; OXIDOREDUCTASE
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	31.87 Å
回转半径 Rg (电子) rg_electron	30.68 Å
零角强度 I(0) i0	311880000.00
分子量 molecular_weight	131850.0 kDa
排除体积 excluded_volume	160710 Å³
包络体积 envelope_volume	198770 Å³
水化壳体积 shell_volume	51298 Å³
包络直径 envelope_diameter	94.9 Å
壳层 Rg shell_rg	39.82 Å
包络 Rg envelope_rg	30.60 Å
形状 Rg shape_rg	30.69 Å
总 Rg total_rg	31.34 Å
总原子数 total_atoms	9272
残基数 n_residues	1182
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	95.6 Å
Rg (实空间) rg_real	31.60 Å
Rg 误差 (实空间) rg_real_error	0.42 Å
I(0) (实空间) i0_real	3.1190e+08
I(0) 误差 (实空间) i0_real_error	4.6610e+06
Rg (倒空间) rg_reciprocal	31.72 Å
I(0) (倒空间) i0_reciprocal	311900000.0000
解质量估计 total_estimate	0.9080
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	42.1 Å
偏度 Skewness skewness	0.042
峰度 Kurtosis kurtosis	-0.616
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	114300000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.990

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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	MALATE DEHYDROGENASE
分子量 formula_weight	32566.3 kDa
EC 编号 ec_number	1.1.1.37
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	10011

TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVSVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVSLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS

来源 Source

来源生物 organism	HALOARCULA MARISMORTUI
NCBI 分类编号 ncbi_taxonomy_id	2238
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 3 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	677

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1o6za1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.5 — LDH N-terminal domain-like

结构域编号 domain_id	d1o6za2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.162 — LDH C-terminal domain-like
超家族 Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
家族 Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

结构域编号 domain_id	d1o6zb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.5 — LDH N-terminal domain-like

结构域编号 domain_id	d1o6zb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.162 — LDH C-terminal domain-like
超家族 Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
家族 Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

结构域编号 domain_id	d1o6zc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.5 — LDH N-terminal domain-like

结构域编号 domain_id	d1o6zc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.162 — LDH C-terminal domain-like
超家族 Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
家族 Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

结构域编号 domain_id	d1o6zd1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.5 — LDH N-terminal domain-like

结构域编号 domain_id	d1o6zd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.162 — LDH C-terminal domain-like
超家族 Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
家族 Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1o6zA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

结构域编号 domain_id	1o6zA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1o6zB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

结构域编号 domain_id	1o6zB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1o6zC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

结构域编号 domain_id	1o6zC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1o6zD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

结构域编号 domain_id	1o6zD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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7. 引用文献 (6)

;The Oligomeric States of Haloarcula Marismortui Malate Dehydrogenase are Modulated by Solvent Components as Shown by Crystallographic and Biochemical Studies ;

J.Mol.Biol. (2003)

PMID: 12581646 · DOI: 10.1016/S0022-2836(02)01450-X PRIMARY

;Insights Into the Molecular Relationships between Malate and Lactate Dehydrogenases: Structural and Biochemical Properties of Monomeric and Dimeric Intermediates of a Mutant of Tetrameric L-[Ldh-Like] Malate Dehydrogenase from the Halophilic Archaeon Haloarcula Marismortui ;

Biochemistry (2000)

PMID: 10653644 · DOI: 10.1021/BI9910023

;Halophilic Adaptation: Novel Solvent Protein Interactions Observed in the 2.9 And 2.6 A Resolution Structures of the Wild Type and a Mutant of Malate Dehydrogenase from Haloarcula Marismortui ;

Biochemistry (2000)

PMID: 10653643 · DOI: 10.1021/BI991001A

Structural Features that Stabilize Halophilic Malate Dehydrogenase from an Archaebacterium

Science (1995)

PMID: 17812611 · DOI: 10.1126/SCIENCE.267.5202.1344

;Mutation at a Single Acidic Amino Acid Enhances the Halophilic Behaviour of Malate Dehydrogenase from Haloarcula Marismortui in Physiological Salts ;

Eur.J.Biochem. (1995)

PMID: 7601139 · DOI: 10.1111/J.1432-1033.1995.TB20659.X

;Cloning, Sequencing, and Expression in Escherichia Coli of the Gene Coding for Malate Dehydrogenase of the Extremely Halophilic Archaebacterium Haloarcula Marismortui ;

Biochemistry (1993)

PMID: 8476859 · DOI: 10.1021/BI00067A020

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晶胞边长 a length_a	126.640 Å
晶胞边长 b length_b	114.420 Å
晶胞边长 c length_c	124.870 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	93.11 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.950 Å
最低分辨率 resolution_low	12.000 Å
R 因子 r_factor	0.1936
R_work r_work	0.1899
R_free r_free	0.2633

fit	/app/data/saxs_computation/o6/1o6z/1o6z.fit
pddf	/app/data/pr_computation/o6/1o6z/1o6z.pr.out
profile	/app/data/saxs_computation/o6/1o6z/1o6z.dat