1rp5

PBP2x from Streptococcus pneumoniae strain 5259 with reduced susceptibility to beta-lactam antibiotics

Method: X-RAY DIFFRACTION D_max: 152.7 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	1rp5
沉积日期 deposition_date	2003-12-03
结构标题 title	PBP2x from Streptococcus pneumoniae strain 5259 with reduced susceptibility to beta-lactam antibiotics
关键词 keywords	PENICILLIN-BINDING PROTEIN, TRANSPEPTIDASE, ANTIBIOTIC RESISTANCE, PEPTIDOGLYCAN SYNTHESIS, CELL WALL, TRANSMEMBRANE; TRANSPEPTIDASE
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	48.40 Å
回转半径 Rg (电子) rg_electron	49.27 Å
零角强度 I(0) i0	326864000.00
分子量 molecular_weight	146080.0 kDa
排除体积 excluded_volume	181460 Å³
包络体积 envelope_volume	250370 Å³
水化壳体积 shell_volume	46905 Å³
包络直径 envelope_diameter	163.3 Å
壳层 Rg shell_rg	46.01 Å
包络 Rg envelope_rg	48.20 Å
形状 Rg shape_rg	49.24 Å
总 Rg total_rg	49.26 Å
总原子数 total_atoms	10270
残基数 n_residues	1367
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	152.7 Å
Rg (实空间) rg_real	49.22 Å
Rg 误差 (实空间) rg_real_error	1.74 Å
I(0) (实空间) i0_real	3.2690e+08
I(0) 误差 (实空间) i0_real_error	6.2390e+06
Rg (倒空间) rg_reciprocal	48.41 Å
I(0) (倒空间) i0_reciprocal	326500000.0000
解质量估计 total_estimate	0.7404
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	32.4 Å
偏度 Skewness skewness	0.501
峰度 Kurtosis kurtosis	-0.704
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	36910000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.682; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.576; Smooth: 0.001

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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 (3)

Entity 1 polymer

描述 description	penicillin-binding protein 2x
分子量 formula_weight	76906.0 kDa
EC 编号 ec_number	3.4.-.-
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	10315

GTGTRFGTDLAKEAKKVHQTTRTVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELETAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEKDRLGNIVPGTEQVSQQTVDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAMSAFGQGISVTQTQMLRAFTAIANDGVMLEPKFISALYDPNDQSVRKSQKEIVGNPVSKEAASVTRDHMVMVGTDPTYGTMYNHSTGKATVNVPGQNVALKSGTAEIADEKNGGYLTGSTNNIFSVVSMHPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKESLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETFAKWLNIELEFEGSGSTVQKQDVRANTAIKDIKKIKLTLGD

来源 Source

来源生物 organism	Streptococcus pneumoniae
NCBI 分类编号 ncbi_taxonomy_id	1313
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	45

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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	d1rp5a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
超家族 Superfamily superfamily	d.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
家族 Family family	d.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain

结构域编号 domain_id	d1rp5a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
超家族 Superfamily superfamily	d.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
家族 Family family	d.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain

结构域编号 domain_id	d1rp5a3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.175 — Penicillin binding protein dimerisation domain
超家族 Superfamily superfamily	d.175.1 — Penicillin binding protein dimerisation domain
家族 Family family	d.175.1.1 — Penicillin binding protein dimerisation domain

结构域编号 domain_id	d1rp5a4
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.3 — beta-lactamase/transpeptidase-like
超家族 Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
家族 Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

结构域编号 domain_id	d1rp5b1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
超家族 Superfamily superfamily	d.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
家族 Family family	d.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain

结构域编号 domain_id	d1rp5b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
超家族 Superfamily superfamily	d.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
家族 Family family	d.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain

结构域编号 domain_id	d1rp5b3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.175 — Penicillin binding protein dimerisation domain
超家族 Superfamily superfamily	d.175.1 — Penicillin binding protein dimerisation domain
家族 Family family	d.175.1.1 — Penicillin binding protein dimerisation domain

结构域编号 domain_id	d1rp5b4
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.3 — beta-lactamase/transpeptidase-like
超家族 Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
家族 Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

CATH v4.4 (8 domains)

结构域编号 domain_id	1rp5A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
同源超家族 H-superfamily homologous superfamily	70 —

结构域编号 domain_id	1rp5A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1310 — Penicillin-binding protein 2a (Domain 2)
同源超家族 H-superfamily homologous superfamily	10 — Penicillin-binding protein 2a (Domain 2)

结构域编号 domain_id	1rp5A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	2110 —

结构域编号 domain_id	1rp5A04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	710 — Beta-lactamase
同源超家族 H-superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

结构域编号 domain_id	1rp5B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
同源超家族 H-superfamily homologous superfamily	70 —

结构域编号 domain_id	1rp5B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1310 — Penicillin-binding protein 2a (Domain 2)
同源超家族 H-superfamily homologous superfamily	10 — Penicillin-binding protein 2a (Domain 2)

结构域编号 domain_id	1rp5B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	2110 —

结构域编号 domain_id	1rp5B04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	710 — Beta-lactamase
同源超家族 H-superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

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7. 引用文献 (5)

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晶胞边长 a length_a	194.989 Å
晶胞边长 b length_b	194.989 Å
晶胞边长 c length_c	154.245 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 42 2 2
空间群编号 int_tables_number	93
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	42.000 Å
R 因子 r_factor	—
R_work r_work	0.2310
R_free r_free	0.2560

fit	/app/data/saxs_computation/rp/1rp5/1rp5.fit
pddf	/app/data/pr_computation/rp/1rp5/1rp5.pr.out
profile	/app/data/saxs_computation/rp/1rp5/1rp5.dat