1k25

PBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae Clinical Isolate

Method: X-RAY DIFFRACTION D_max: 160.3 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1k25
沉积日期 deposition_date	2001-09-26
结构标题 title	PBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae Clinical Isolate
关键词 keywords	antibiotic resistance, clinical mutant, low-affinity penicillin-binding, MEMBRANE PROTEIN; MEMBRANE PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	48.96 Å
回转半径 Rg (电子) rg_electron	48.84 Å
零角强度 I(0) i0	840708000.00
分子量 molecular_weight	238260.0 kDa
排除体积 excluded_volume	296940 Å³
包络体积 envelope_volume	426250 Å³
水化壳体积 shell_volume	73202 Å³
包络直径 envelope_diameter	164.7 Å
壳层 Rg shell_rg	53.30 Å
包络 Rg envelope_rg	46.86 Å
形状 Rg shape_rg	48.82 Å
总 Rg total_rg	49.07 Å
总原子数 total_atoms	16765
残基数 n_residues	2237
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

▼

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

最大尺寸 Dmax dmax	160.3 Å
Rg (实空间) rg_real	48.79 Å
Rg 误差 (实空间) rg_real_error	1.32 Å
I(0) (实空间) i0_real	8.4070e+08
I(0) 误差 (实空间) i0_real_error	1.6670e+07
Rg (倒空间) rg_reciprocal	48.96 Å
I(0) (倒空间) i0_reciprocal	840900000.0000
解质量估计 total_estimate	0.8239
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	70.1 Å
偏度 Skewness skewness	0.116
峰度 Kurtosis kurtosis	-0.629
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	93510000.0000
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: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

▶

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

▶

5. 实体与聚合体信息 (2)

Entity 1 polymer

描述 description	low-affinity PENICILLIN-BINDING PROTEIN 2X
分子量 formula_weight	75259.4 kDa
突变 mutation	F364L
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	16786

HQITRTVPAKRGTIYDRNGVPIAEDATSYNVYAVIDKKYKSATGKILYVEDAQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGSKGNGITYANMMAIKKELETAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEKDRVGNIVPGTELVSQQTVDGKDVYTTLSSPLQSFMETQMDAFLEKVKGKYMTATLVSAKTGEILATTQRPTFNADTKEGITEDFVWRDILYQSNYEPGSAMKVMTLASSIDNNTFPSGEYFNSSELKIADATTRDWDVNEGLTTGGMMTFLQGFAHSSNVGMSLLEQKMGDATWLDYLKRFKFGVPTRFGLTDEYAGQLPADNIVSIAQSSFGQGISVTQTQMLRAFTAIANDGVMLEPKFISAIYDTNNQSVRKSQKEIVGNPVSKEAASTTRNHMILVGTDPLYGTMYNHYTGKPIITVPGQNVAVKSGTAQIADEKNGGYLVGSTNYIFSAVTMNPAENPDFILYVTVQQPEHYSGIQLGEFATPILERASAMKESLNLQSPAKNLDKVTTESSYAMPSIKDISPGELAEALRRNIVQPIVVGTGTKIKETSVEEGTNLAPNQQVLLLSDKVEEIPDMYGWKKETAETFAKWLDIELEFEGSGSVVQKQDVRTNTAIKNIKKIKLTLGD

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 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	21

▼

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

结构域编号 domain_id	d1k25a1
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	d1k25a2
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	d1k25a3
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	d1k25a4
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	d1k25b1
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	d1k25b2
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	d1k25b3
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	d1k25b4
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	d1k25c1
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	d1k25c2
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	d1k25c3
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	d1k25c4
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	d1k25d1
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	d1k25d2
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	d1k25d3
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	d1k25d4
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	1k25A01
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	1k25A02
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	1k25B01
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	1k25B02
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	1k25C01
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	1k25C02
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	1k25D01
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	1k25D02
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

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	146.560 Å
晶胞边长 b length_b	146.560 Å
晶胞边长 c length_c	132.610 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 32
空间群编号 int_tables_number	145
晶系 crystal_system	—

分辨率 resolution	3.200 Å
最低分辨率 resolution_low	19.900 Å
R 因子 r_factor	0.2350
R_work r_work	0.2350
R_free r_free	0.3120

fit	/app/data/saxs_computation/k2/1k25/1k25.fit
pddf	/app/data/pr_computation/k2/1k25/1k25.pr.out
profile	/app/data/saxs_computation/k2/1k25/1k25.dat

PBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae Clinical Isolate

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