1mwr

;Structure of SeMet Penicillin binding protein 2a from methicillin resistant Staphylococcus aureus strain 27r (trigonal form) at 2.45 A resolution. ;

Method: X-RAY DIFFRACTION D_max: 131.6 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1mwr
沉积日期 deposition_date	2002-10-01
结构标题 title	;Structure of SeMet Penicillin binding protein 2a from methicillin resistant Staphylococcus aureus strain 27r (trigonal form) at 2.45 A resolution. ;
关键词 keywords	penicillin binding protein, beta-lactam, d, d-transpeptidase, d-carboxypeptidase, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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	39.85 Å
回转半径 Rg (电子) rg_electron	39.53 Å
零角强度 I(0) i0	327797000.00
分子量 molecular_weight	145080.0 kDa
排除体积 excluded_volume	180070 Å³
包络体积 envelope_volume	237810 Å³
水化壳体积 shell_volume	50850 Å³
包络直径 envelope_diameter	134.4 Å
壳层 Rg shell_rg	44.15 Å
包络 Rg envelope_rg	39.20 Å
形状 Rg shape_rg	39.52 Å
总 Rg total_rg	39.80 Å
总原子数 total_atoms	10081
残基数 n_residues	1223
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	131.6 Å
Rg (实空间) rg_real	39.86 Å
Rg 误差 (实空间) rg_real_error	1.38 Å
I(0) (实空间) i0_real	3.2780e+08
I(0) 误差 (实空间) i0_real_error	5.9570e+06
Rg (倒空间) rg_reciprocal	39.86 Å
I(0) (倒空间) i0_reciprocal	327800000.0000
解质量估计 total_estimate	0.8259
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	49.4 Å
偏度 Skewness skewness	0.258
峰度 Kurtosis kurtosis	-0.585
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	53590000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; 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 (4)

Entity 1 polymer

描述 description	penicillin-binding protein 2a
分子量 formula_weight	74574.5 kDa
突变 mutation	Y23M, delta 1-22
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	10089

MASKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI 分类编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	CADMIUM ION
分子量 formula_weight	112.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 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	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	8

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1mwra1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.5 — Penicillin binding protein 2a (PBP2A), N-terminal domain

结构域编号 domain_id	d1mwra2
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	d1mwra3
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	d1mwrb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.5 — Penicillin binding protein 2a (PBP2A), N-terminal domain

结构域编号 domain_id	d1mwrb2
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	d1mwrb3
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	1mwrA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	100 — NTF2-like; domain 1

结构域编号 domain_id	1mwrA02
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	1mwrA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1390 — Ribosomal Protein L30; Chain: A,
同源超家族 H-superfamily homologous superfamily	30 — Penicillin-binding protein 2a; domain 3

结构域编号 domain_id	1mwrA04
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	1mwrB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	100 — NTF2-like; domain 1

结构域编号 domain_id	1mwrB02
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	1mwrB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1390 — Ribosomal Protein L30; Chain: A,
同源超家族 H-superfamily homologous superfamily	30 — Penicillin-binding protein 2a; domain 3

结构域编号 domain_id	1mwrB04
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 (1)

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晶胞边长 a length_a	141.060 Å
晶胞边长 b length_b	141.060 Å
晶胞边长 c length_c	146.671 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 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	2.450 Å
最低分辨率 resolution_low	24.890 Å
R 因子 r_factor	0.2700
R_work r_work	0.2700
R_free r_free	0.3240

fit	/app/data/saxs_computation/mw/1mwr/1mwr.fit
pddf	/app/data/pr_computation/mw/1mwr/1mwr.pr.out
profile	/app/data/saxs_computation/mw/1mwr/1mwr.dat