8poy

;Crystal Structure of the C120G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the air-oxidized state at 1.93 A Resolution. ;

Method: X-RAY DIFFRACTION D_max: 80.2 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	8poy
沉积日期 deposition_date	2023-07-05
最后修订 last_revision	2025-02-26
结构标题 title	;Crystal Structure of the C120G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the air-oxidized state at 1.93 A Resolution. ;
关键词 keywords	;[NIFE]-HYDROGENASE, HYDROGENASE, OXYGEN-TOLERANCE, HYDROGEN CATALYSIS, KNALLGASBACTERIA, PROTEOBACTERIA, METALLOENZYME, BIMETALLIC, NI-FE ACTIVE SITE, [4FE-3S], PROXIMAL CLUSTER, AEROBIC HYDROGEN BACTERIA, OXIDOREDUCTASE, ELECTRON TRANSFER, METALLOPROTEIN, CATALYTIC CENTER, MEMBRANE, MEMBRANE-BOUND, OXIDOREDUCTASE-OXIDOREDUCTASE COMPLEX, ELECTRON RELAY, CUBANE CLUSTER, CLUSTER TUNING, ELECTRON TRANSPORT, AS-ISOLATED STATE, AIR-OXIDIZED-STATE ;; 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	26.54 Å
回转半径 Rg (电子) rg_electron	25.46 Å
零角强度 I(0) i0	158859000.00
分子量 molecular_weight	97381.0 kDa
排除体积 excluded_volume	120590 Å³
包络体积 envelope_volume	135280 Å³
水化壳体积 shell_volume	41087 Å³
包络直径 envelope_diameter	83.5 Å
壳层 Rg shell_rg	35.25 Å
包络 Rg envelope_rg	25.89 Å
形状 Rg shape_rg	25.48 Å
总 Rg total_rg	26.27 Å
总原子数 total_atoms	6799
残基数 n_residues	863
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	80.2 Å
Rg (实空间) rg_real	26.34 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	1.5890e+08
I(0) 误差 (实空间) i0_real_error	2.3070e+06
Rg (倒空间) rg_reciprocal	26.41 Å
I(0) (倒空间) i0_reciprocal	158900000.0000
解质量估计 total_estimate	0.9030
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	33.4 Å
偏度 Skewness skewness	0.111
峰度 Kurtosis kurtosis	-0.515
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	43040000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.986

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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 (10)

Entity 1 polymer

描述 description	Uptake hydrogenase large subunit
分子量 formula_weight	67247.2 kDa
EC 编号 ec_number	1.12.99.6
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	L
原子数 atom_count	7311

MSAYATQGFNLDDRGRRIVVDPVTRIEGHMRCEVNVDANNVIRNAVSTGTMWRGLEVILKGRDPRDAWAFVERICGVCTGCHALASVRAVENALDIRIPKNAHLIREIMAKTLQVHDHAVHFYHLHALDWVDVMSALKADPKRTSELQQLVSPAHPLSSAGYFRDIQNRLKRFVESGQLGPFMNGYWGSKAYVLPPEANLMAVTHYLEALDLQKEWVKIHTIFGGKNPHPNYLVGGVPCAINLDGIGAASAPVNMERLSFVKARIDEIIEFNKNVYVPDVLAIGTLYKQAGWLYGGGLAATNVLDYGEYPNVAYNKSTDQLPGGAILNGNWDEVFPVDPRDSQQVQEFVSHSWYKYADESVGLHPWDGVTEPNYVLGANTKGTRTRIEQIDESAKYSWIKSPRWRGHAMEVGPLSRYILAYAHARSGNKYAERPKEQLEYSAQMINSAIPKALGLPETQYTLKQLLPSTIGRTLARALESQYCGEMMHSDWHDLVANIRAGDTATANVDKWDPATWPLQAKGVGTVAAPRGALGHWIRIKDGRIENYQCVVPTTWNGSPRDYKGQIGAFEASLMNTPMVNPEQPVEILRTLHSFDPCLACSTH

来源 Source

来源生物 organism	Cupriavidus necator H16
NCBI 分类编号 ncbi_taxonomy_id	381666
宿主生物 host_organism	Cupriavidus necator H16

Entity 2 polymer

描述 description	Uptake hydrogenase small subunit
分子量 formula_weight	35980.9 kDa
EC 编号 ec_number	1.12.99.6
突变 mutation	C120G
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	S

METKPRTPVLWLHGLECTCCSESFIRSAHPLAKDVVLSMISLDYDDTLMAAAGHQAEAILEEIMTKYKGNYILAVEGNPPLNQDGMSCIIGGRPFIEQLKYVAKDAKAIISWGSCASWGGVQAAKPNPTQATPVHKVITDKPIIKVPGCPPIAEVMTGVITYMLTFDRIPELDRQGRPKMFYSQRIHDKCYRRPHFDAGQFVEEWDDESARKGFCLYKMGCKGPTTYNACSTTRWNEGTSFPIQSGHGCIGCSEDGFWDKGSFYDRLTGISQFGVEANADKIGGTASVVVGAAVTAHAAASAIKRASKKNETSGSEHRSAWSHPQFEK

来源 Source

来源生物 organism	Cupriavidus necator H16
NCBI 分类编号 ncbi_taxonomy_id	381666
宿主生物 host_organism	Cupriavidus necator H16

Entity 3 non-polymer

描述 description	NI-FE OXIDIZED ACTIVE CENTER
分子量 formula_weight	210.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	FE3-S4 CLUSTER
分子量 formula_weight	295.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 non-polymer

描述 description	FE4-S3 CLUSTER
分子量 formula_weight	319.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 9 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	1

Entity 10 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	444

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7. 引用文献 (1)

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晶胞边长 a length_a	73.169 Å
晶胞边长 b length_b	95.633 Å
晶胞边长 c length_c	119.927 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	4

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	1.930 Å
最低分辨率 resolution_low	74.770 Å
R 因子 r_factor	0.1551
R_work r_work	0.1535
R_free r_free	0.1843

fit	/app/data/saxs_computation/po/8poy/8poy.fit
pddf	/app/data/pr_computation/po/8poy/8poy.pr.out
profile	/app/data/saxs_computation/po/8poy/8poy.dat

;Crystal Structure of the C120G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the air-oxidized state at 1.93 A Resolution. ;

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 (10)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)