3HNO | pdb_00003hno

Crystal Structure of Pyrophosphate-dependent phosphofructokinase from Nitrosospira multiformis. Northeast Structural Genomics Consortium target id NmR42

PDB DOI: https://doi.org/10.2210/pdb3HNO/pdb

Classification: TRANSFERASE
Organism(s): Nitrosospira multiformis ATCC 25196
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-31 Released: 2009-06-30
Deposition Author(s): Seetharaman, J., Abashidze, M., Sahdev, S., Janjua, H., Xiao, R., Ciccosanti, C., Foote, E.L., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.241 (Depositor), 0.247 (DCC)
R-Value Work:
0.216 (Depositor), 0.221 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Pyrophosphate-dependent phosphofructokinase from Nitrosospira multiformis. Northeast Structural Genomics Consortium target id NmR42

Seetharaman, J., Abashidze, M., Sahdev, S., Janjua, H., Xiao, R., Ciccosanti, C., Foote, E.L., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 180.53 kDa
Atom Count: 12,308
Modeled Residue Count: 1,579
Deposited Residue Count: 1,676
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrophosphate-dependent phosphofructokinase	A, B, C, D	419	Nitrosospira multiformis ATCC 25196	Mutation(s): 0 Gene Names: Nmul_A0740 EC: 2.7.1.90
UniProt
Find proteins for Q2YB24 (Nitrosospira multiformis (strain ATCC 25196 / NCIMB 11849 / C 71)) Explore Q2YB24 Go to UniProtKB: Q2YB24
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2YB24
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.241 (Depositor), 0.247 (DCC)
R-Value Work: 0.216 (Depositor), 0.221 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.895	α = 90
b = 89.322	β = 119.12
c = 115.462	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SHELXS	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-06-30

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations