SAXSdb — 7zul

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Penicillin-binding protein 1b

Streptococcus pneumoniae R6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	6-azido-N-[(2R)-1-oxidanylidene-1-[[(2S,3R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]amino]-3-phenyl-propan-2-yl]hexanamide × 1 CHLORIDE ION × 27 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7CRA4_STRR6
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 1–821； UniProt 1–821

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7zul
Deposition date deposition_date	2022-05-12
Structure title title	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with 8Az lactone - Streptococcus pneumoniae R6
Keywords keywords	CELL WALL, PEPTIDOGLYCAN SYNTHESIS ENZYME, INFECTION, DRUG-BINDING PROTEIN, LACTAM ANTIBIOTICS, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7zul__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7zul__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7zul__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	24.69 Å
Rg (electron density)	23.96 Å
Total Rg	24.70 Å
Atom count	3561
Residues	454
Excluded volume	62834 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7zul__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Penicillin-binding protein 1b
Molecular weight formula_weight	89461.2 kDa
EC 编号 ec_number	2.3.2.-,2.4.1.129
Mutation mutation	N656G R686Q R687Q
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA
Atom count atom_count	3978

MQNQLNELKRKMLEFFQQKQKNKKSARPGKKGSSTKKSKTLDKSAIFPAILLSIKALFNLLFVLGFLGGMLGAGIALGYGVALFDKVRVPQTEELVNQVKDISSISEITYSDGTVIASIESDLLRTSISSEQISENLKKAIIATEDEHFKEHKGVVPKAVIRATLGKFVGLGSSSGGSTLTQQLIKQQVVGDAPTLARKAAEIVDALALERAMNKDEILTTYLNVAPFGRNNKGQNIAGARQAAEGIFGVDASQLTVPQAAFLAGLPQSPITYSPYENTGELKSDEDLEIGLRRAKAVLYSMYRTGALSKDEYSQYKDYDLKQDFLPSGTVTGISRDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTGQDENMWLMLSTPRLTLGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSLPTPSSSSSSSSSSSDSSNSSTTRPSSSRARR

Source Source

Source organism organism	Streptococcus pneumoniae R6
NCBI taxonomy ID ncbi_taxonomy_id	171101
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	6-azido-N-[(2R)-1-oxidanylidene-1-[[(2S,3R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]amino]-3-phenyl-propan-2-yl]hexanamide
Molecular weight formula_weight	389.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	27

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	383

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Unit-cell length a length_a	96.934 Å
Unit-cell length b length_b	149.773 Å
Unit-cell length c length_c	98.872 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.744 Å
Low-resolution limit resolution_low	42.251 Å
R factor r_factor	—
R_work r_work	0.1802
R_free r_free	0.2063

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with 8Az lactone - Streptococcus pneumoniae R6

1. Protein Identity and Related Structures Protein Identity & Related Structures

Penicillin-binding protein 1b

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7zul__assembly_1__model_1

7zul__assembly_1__model_1 | I(q)

7zul__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with 8Az lactone - Streptococcus pneumoniae R6

1. Protein Identity and Related Structures Protein Identity & Related Structures

Penicillin-binding protein 1b

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7zul__assembly_1__model_1

7zul__assembly_1__model_1 | I(q)

7zul__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)