5IBX | pdb_00005ibx

1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (TIM) from Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb5IBX/pdb

Classification: ISOMERASE
Organism(s): Streptococcus pneumoniae D39
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-02-22 Released: 2016-03-09
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Flores, K., Shatsman, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.232 (Depositor), 0.240 (DCC)
R-Value Work:
0.196 (Depositor), 0.204 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (TIM) from Streptococcus pneumoniae

Minasov, G., Shuvalova, L., Dubrovska, I., Flores, K., Shatsman, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases

To be published.

Macromolecule Content

Total Structure Weight: 215.46 kDa
Atom Count: 17,739
Modeled Residue Count: 1,999
Deposited Residue Count: 2,040
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B, D, E, H	255	Streptococcus pneumoniae D39	Mutation(s): 0 Gene Names: tpiA, SPD_1404 EC: 5.3.1.1
UniProt
Find proteins for Q04JH4 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore Q04JH4 Go to UniProtKB: Q04JH4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04JH4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	C, F, G	255	Streptococcus pneumoniae D39	Mutation(s): 0 Gene Names: tpiA, SPD_1404 EC: 5.3.1.1
UniProt
Find proteins for Q04JH4 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore Q04JH4 Go to UniProtKB: Q04JH4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04JH4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain S [auth F] SDF format, chain T [auth G] SDF format, chain U [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] MOL2 format, chain T [auth G] MOL2 format, chain U [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth F] mmCIF format, chain T [auth G] mmCIF format, chain U [auth H]	I [auth A] J [auth B] K [auth B] L [auth C] M [auth C] I [auth A], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth F], T [auth G], U [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A, B, D, E, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.232 (Depositor), 0.240 (DCC)
R-Value Work: 0.196 (Depositor), 0.204 (DCC)
R-Value Observed: 0.198 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.845	α = 75.43
b = 84.351	β = 65.97
c = 92.463	γ = 62.03

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary

5IBX | pdb_00005ibx

1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (TIM) from Streptococcus pneumoniae

Literature

1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (TIM) from Streptococcus pneumoniae

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)