7SPM | pdb_00007spm

Replication Initiator Protein REPE54 and cognate DNA sequence with terminal three prime phosphates chemically crosslinked (30 mg/mL EDC, 12 hours, 2 doses).

• PDB DOI: https://doi.org/10.2210/pdb7SPM/pdb
• NAKB: 7SPM

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-11-02 Released: 2021-11-10 
• Deposition Author(s): Ward, A.R., Snow, C.D.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.28 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Stabilizing DNA-Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA

Orun, A.R., Dmytriw, S., Vajapayajula, A., Snow, C.D.

(2022) Crystals (Basel) 12

• DOI: https://doi.org/10.3390/cryst12010049

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.29 kDa 
• Atom Count: 2,649 
• Modeled Residue Count: 265 
• Deposited Residue Count: 307 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RepB family plasmid replication initiator protein	C	263	Escherichia coli	Mutation(s): 1  Gene Names:  repE, RepE, repE_1, repE_2, A9P13_27925, ACN81_13795, AKG29_00005, AM270_25025, AM446_00510, AM465_27515, APX88_12585, B9N33_25510, BANRA_05159, BANRA_05459, BANRA_05682, BANRA_05685, BE930_02070, BE963_00170, BFD68_26000, BIU72_26315, BK334_12915, BON69_00085, BON86_02490, BTQ06_15345, BvCmsKSNP073_00547, BvCmsKSNP081_03109, C5F73_28740, C6669_28055, CCZ17_26065, CDL37_25390, CUB99_27055, D0X26_27580, D2188_23935, D6C57_20535, D6T60_26250, D9G11_25395, D9J60_24770, DL545_01395, DLU82_26460, DM102_26130, DMZ50_25125, DN808_25760, DNQ45_17165, DP277_27365, E0L04_25075, E4K51_24545, E5P24_21725, E5S56_18100, EA191_27055, EA214_24280, EA233_23655, EA834_24495, EC3234A_223c00190, ECTO124_05352, EGT48_00285, EIZ93_24320, EJC75_00275, ELT22_23490, ELT31_24090, ELT31_26285, ELT33_22145, ELU82_24155, ELU85_22525, ELV00_24275, ELV13_22345, ELV22_21715, ELV22_26415, ELV24_23180, ELV24_26400, ELX56_23450, ELX56_26570, ELX68_22815, ELX68_25985, ELX70_23725, ELX70_27680, ELX79_25360, ELX79_27900, ELX83_21670, ELX83_26905, ELY23_22635, ELY23_25820, ELY24_18745, ELY24_28685, ELY48_20420, ELY48_27905, ELY50_22820, ELY50_26360, EPS70_23590, EQ823_22980, EQ830_17775, ERS085362_04815, ERS150873_04643, EVY14_01415, ExPECSC065_01123, F0L67_01685, F7O57_26240, FAF34_003215, FKO60_21690, FVA71_27640, G3565_27065, G4276_24945, G4280_26215, G5603_23890, G5632_20220, G5697_22865, G5V60_25015, GE057_22565, GE087_25865, GE096_23180, GE400_25540, GE558_24730, GKE29_21080, GKE58_20235, GKE60_20510, GKE79_19945, GKE87_19350, GQY14_24020, GRC73_23425, HGR17_18615, HGR87_25030, HGR88_23710, HGS97_17250, HH117_25695, HH456_004544, HH814_004957, HIO03_005020, HIZ44_004944, HJ359_004520, HJI79_004024, HJL93_004672, HJM89_004053, HJT66_004466, HKA14_004545, HL186_24195, HLI97_004832, HMT01_25475, HMT08_23785, HNV94_24925, HNX16_24825, HNX34_21985, HPE39_26560, HR075_24855, HV055_25390, HV303_25935, HVW09_26465, HVW60_23575, HVW98_24555, HVX24_22925, HVX51_24935, HVY93_24645, HVZ71_26895, IB283_25495, IPF_37, pCTXM15_EC8_00107, RCS105_pI0165, RCS57_p0140, RCS59_P0063, SAMEA4370330_00165, SAMEA4370365_00054, SY51_26335, WP4S17E03_P11650, WP4S18E08_P10410, YDC107_5106
UniProt
Find proteins for P03856 (Escherichia coli (strain K12)) Explore P03856  Go to UniProtKB:  P03856

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*A)-3')	A	22	Escherichia coli

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*A)-3')	B	22	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.28 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.817	α = 90
b = 80.174	β = 122.899
c = 74.723	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XSCALE	data scaling
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-10 
Deposition Author(s): Ward, A.R., Snow, C.D.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	2003748

Revision History  

• Version 1.0: 2021-11-10
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-01
  Changes: Database references