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1d2m

UVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME

Method: X-RAY DIFFRACTION D_max: 88.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d2m
deposition_date	1999-09-25
title	UVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME
keywords	MULTIDOMAIN PROTEIN, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	28.20 Å
rg_electron	27.40 Å
i0	64281600.00
molecular_weight	64084.0 kDa
excluded_volume	80889 Å³
envelope_volume	100100 Å³
shell_volume	30822 Å³
envelope_diameter	94.2 Å
shell_rg	34.51 Å
envelope_rg	27.43 Å
shape_rg	27.37 Å
total_rg	28.25 Å
total_atoms	4524
n_residues	552
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	88.8 Å
rg_real	28.18 Å
rg_real_error	0.63 Å
i0_real	6.4280e+07
i0_real_error	9.6430e+05
rg_reciprocal	28.19 Å
i0_reciprocal	64280000.0000
total_estimate	0.9064
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	87.2 Å
skewness	0.279
kurtosis	-0.558
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	16450000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.957

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	EXCINUCLEASE ABC SUBUNIT B
formula_weight	76266.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4859

MTFRYRGPSPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVIEALGRPALVLAPNKILAAQLAAEFRELFPENAVEYFISYYDYYQPEAYVPGKDLYIEKDASINPEIERLRHSTTRSLLTRRDVIVVASVSAIYGLGDPREYRARNLVVERGKPYPREVLLERLLELGYQRNDIDLSPGRFRAKGEVLEIFPAYETEPIRVELFGDEVERISQVHPVTGERLRELPGFVLFPATHYLSPEGLEEILKEIEKELWERVRYFEERGEVLYAQRLKERTLYDLEMLRVMGTCPGVENYARYFTGKAPGEPPYTLLDYFPEDFLVFLDESHVTVPQLQGMYRGDYARKKTLVDYGFRLPSALDNRPLRFEEFLERVSQVVFVSATPGPFELAHSGRVVEQIIRPTGLLDPLVRVKPTENQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEAMQRAIEETNRRRALQEAYNLEHGITPETVRKEVRAVIRPEGYEEAPLEADLSGEDLRERIAELELAMWQAAEALDFERAARLRDEIRALEARLQGVRAPEPVPGGRKRKRR

Source

organism	Thermus thermophilus
ncbi_taxonomy_id	300852
host_organism	Escherichia coli

Entity 2 non-polymer

description	octyl beta-D-glucopyranoside
formula_weight	292.4 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	335

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6. Citations (2)

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length_a	135.040 Å
length_b	135.040 Å
length_c	106.756 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	1.900 Å
resolution_low	30.000 Å
r_factor	0.2340
r_work	0.2340
r_free	0.2530

fit	/app/data/saxs_computation/d2/1d2m/1d2m.fit
pddf	/app/data/pr_computation/d2/1d2m/1d2m.pr.out
profile	/app/data/saxs_computation/d2/1d2m/1d2m.dat

UVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction