Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43130.77 
• Atom Count: 2942 
• Residue Count: 364 
• Unique protein chains: 1

5PNU

PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 223)

• DOI: 10.2210/pdb5PNU/pdb
• Deposition Group: G_1002021 (ground state)

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2017-02-07 Released: 2017-03-15 
• Deposition Author(s): Pearce, N.M., Krojer, T., Talon, R., Bradley, A.R., Fairhead, M., Sethi, R., Wright, N., MacLean, E., Collins, P., Brandao-Neto, J., Douangamath, A., Renjie, Z., Dias, A., Vollmar, M., Ng, J., Szykowska, A., Burgess-Brown, N., Brennan, P.E., Cox, O., Oppermann, U., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.199 
• R-Value Work: 0.179 

Literature

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.

Pearce, N.M., Krojer, T., Bradley, A.R., Collins, P., Nowak, R.P., Talon, R., Marsden, B.D., Kelm, S., Shi, J., Deane, C.M., von Delft, F.

(2017) Nat Commun 8: 15123-15123

• PubMed: 28436492 
• DOI: 10.1038/ncomms15123
• Primary Citation of Related Structures:  
  5PZJ, 5PZI, 5PZH, 5PZG, 5PZF, 5PZE, 5PZD, 5PZC, 5PZB, 5PZA, 5PZ9, 5PZ8, 5PZ7, 5PZ6, 5PZ5, 5PZ4, 5PZ3, 5PZ2, 5PZ1, 5PZ0, 5PYZ, 5PYY, 5PYX, 5PYW, 5PYV, 5PYU, 5PYT, 5PYS, 5PYR, 5PYQ, 5PYP, 5PYO, 5PYN, 5PYM, 5PYL, 5PYK, 5PYJ, 5PYI, 5PYG, 5PYH,
  5PZJ, 5PZI, 5PZH, 5PZG, 5PZF, 5PZE, 5PZD, 5PZC, 5PZB, 5PZA, 5PZ9, 5PZ8, 5PZ7, 5PZ6, 5PZ5, 5PZ4, 5PZ3, 5PZ2, 5PZ1, 5PZ0, 5PYZ, 5PYY, 5PYX, 5PYW, 5PYV, 5PYU, 5PYT, 5PYS, 5PYR, 5PYQ, 5PYP, 5PYO, 5PYN, 5PYM, 5PYL, 5PYK, 5PYJ, 5PYI, 5PYG, 5PYH, 5PYF, 5PYE, 5PYD, 5PYC, 5PYA, 5PYB, 5PY9, 5PY8, 5PY7, 5PY6, 5PY5, 5PY4, 5PY3, 5PY2, 5PY1, 5PY0, 5PXZ, 5PXY, 5PXX, 5PXV, 5PXW, 5PXU, 5PXT, 5PXS, 5PXR, 5PXQ, 5PXP, 5PXO, 5PXN, 5PXM, 5PXL, 5PXK, 5PXJ, 5PXI, 5PXH, 5PXG, 5PXF, 5PXE, 5PXD, 5PXC, 5PXB, 5PXA, 5PX9, 5PX8, 5PX7, 5PX6, 5PX5, 5PX4, 5PX3, 5PX2, 5PX1, 5PX0, 5PWZ, 5PWY, 5PWX, 5PWW, 5PWV, 5PWU, 5PWT, 5PWS, 5PWR, 5PWQ, 5PWP, 5PWO, 5PWN, 5PWM, 5PWL, 5PWK, 5PWJ, 5PWI, 5PWH, 5PWG, 5PWF, 5PWE, 5PWC, 5PWD, 5PWB, 5PWA, 5PW9, 5PW6, 5PW7, 5PW8, 5PW5, 5PW4, 5PW3, 5PW2, 5PW1, 5PW0, 5PVZ, 5PVY, 5PVX, 5PVW, 5PVV, 5PVU, 5PVT, 5PVS, 5PVR, 5PVQ, 5PVP, 5PVO, 5PVN, 5PVM, 5PVL, 5PVK, 5PVJ, 5PVI, 5PVH, 5PVG, 5PVF, 5PVE, 5PVD, 5PVC, 5PVB, 5PVA, 5PV9, 5PV7, 5PV8, 5PV6, 5PV5, 5PV4, 5PV3, 5PV2, 5PV1, 5PV0, 5PUZ, 5PUY, 5PUX, 5PUW, 5PUV, 5PUU, 5PUT, 5PUS, 5PUR, 5PUQ, 5PUP, 5PUO, 5PUN, 5PUM, 5PUL, 5PUK, 5PUJ, 5PUI, 5PUH, 5PUG, 5PUF, 5PUE, 5PUD, 5PUC, 5PUB, 5PUA, 5PU9, 5PU8, 5PU7, 5PU6, 5PU5, 5PU4, 5PU3, 5PU2, 5PU1, 5PU0, 5PTZ, 5PTY, 5PTX, 5PTW, 5PTV, 5PTU, 5PTT, 5PTS, 5PTR, 5PTQ, 5PTO, 5PTN, 5PTM, 5PTL, 5PTK, 5PTJ, 5PTH, 5PTG, 5PTF, 5PTE, 5PTC, 5PTB, 5PTA, 5PT9, 5PT8, 5PT7, 5PT6, 5PT5, 5PT4, 5PT3, 5PT2, 5PT1, 5PT0, 5PSZ, 5PSY, 5PSX, 5PSW, 5PSV, 5PSU, 5PST, 5PSS, 5PSR, 5PSQ, 5PSP, 5PSO, 5PSN, 5PSM, 5PSL, 5PSK, 5PSJ, 5PSI, 5PSH, 5PSG, 5PSF, 5PSE, 5PSD, 5PSC, 5PSB, 5PSA, 5PS9, 5PS8, 5PS7, 5PS6, 5PS5, 5PS4, 5PS3, 5PS2, 5PS1, 5PS0, 5PRZ, 5PRY, 5PRX, 5PRW, 5PRV, 5PRU, 5PRT, 5PRS, 5PRR, 5PRQ, 5PRP, 5PRO, 5PRM, 5PRL, 5PRK, 5PRJ, 5PRI, 5PRH, 5PRG, 5PRF, 5PRE, 5PRD, 5PRB, 5PRA, 5PR9, 5PR8, 5PR7, 5PR6, 5PR5, 5PR4, 5PR2, 5PR1, 5PR0, 5PQZ, 5PQY, 5PQX, 5PQW, 5PQV, 5PQU, 5PQT, 5PQS, 5PQR, 5PQQ, 5PQP, 5PQN, 5PQO, 5PQM, 5PQL, 5PQK, 5PQJ, 5PQI, 5PQH, 5PQF, 5PQG, 5PQE, 5PQD, 5PQC, 5PQB, 5PQA, 5PQ9, 5PQ8, 5PQ7, 5PQ5, 5PQ6, 5PQ4, 5PQ3, 5PQ2, 5PQ1, 5PQ0, 5PPZ, 5PPY, 5PPX, 5PPW, 5PPV, 5PPU, 5PPT, 5PPS, 5PPR, 5PPQ, 5PPP, 5PPO, 5PPN, 5PPM, 5PPL, 5PPK, 5PPJ, 5PPI, 5PPH, 5PPG, 5PPF, 5PPE, 5PPD, 5PPC, 5PPB, 5PPA, 5PP9, 5PP8, 5PP7, 5PP6, 5PP5, 5PP4, 5PP3, 5PP2, 5PP1, 5PP0, 5POZ, 5POY, 5POX, 5POW, 5POV, 5POU, 5POT, 5POS, 5POR, 5POQ, 5POP, 5POO, 5PON, 5POM, 5POK, 5POL, 5POJ, 5POI, 5POH, 5POG, 5POF, 5POE, 5POD, 5POC, 5POB, 5POA, 5PO9, 5PO8, 5PO7, 5PO6, 5PO5, 5PO4, 5PO3, 5PO2, 5PO1, 5PO0, 5PNZ, 5PNY, 5PNX, 5PNW, 5PNV, 5PNS, 5PNR, 5PNQ, 5PNP, 5PNO, 5PNN, 5PNM, 5PNL, 5PNK, 5PNJ, 5PNI, 5PNH, 5PNG, 5PNF, 5PNE, 5PND, 5PNC, 5PNB, 5PNA, 5PN9, 5PN8, 5PN7, 5PN6, 5PN5, 5PN4, 5PN3, 5PN2, 5PN1, 5PN0, 5PMZ, 5PMY, 5PMX, 5PMW, 5PMV, 5PMU, 5PMT, 5PMS, 5PMR, 5PMQ, 5PMP, 5PMO, 5PMN, 5PMM, 5PML, 5PMK, 5PMJ, 5PMI, 5PMH, 5PMG, 5PMF, 5PME, 5PMD, 5PMC, 5PMB, 5PMA, 5PM9, 5PM8, 5PM7, 5PM6, 5PM5, 5PM4, 5PM3, 5PM2, 5PM1, 5PM0, 5PLZ, 5PLY, 5PLX, 5PLW, 5PLV, 5PLU, 5PLT, 5PLS, 5PLR, 5PLQ, 5PLP, 5PLO, 5PLN, 5PLM, 5PLL, 5PLK, 5PLJ, 5PLI, 5PLH, 5PLG, 5PLF, 5PLE, 5PLD, 5PLC, 5PLB, 5PLA, 5PL9, 5PL8, 5PL7, 5PL6, 5PL5, 5PL4, 5PL3, 5PL2, 5PL1, 5PL0, 5PKZ, 5PKY, 5PKX, 5PKW, 5PKV, 5PKU, 5PKT, 5PKS, 5PKR, 5PKQ, 5PKP, 5PKO, 5PKN, 5PKM, 5PKL, 5PKK, 5PKJ, 5PKI, 5PKH, 5PKG, 5PKF, 5PKE, 5PKD, 5PKC, 5PKB, 5PKA, 5PK9, 5PK8, 5PK7, 5PK6, 5PK5, 5PK4, 5PK3, 5PK2, 5PK1, 5PK0, 5PJZ, 5PJY, 5PJX, 5PJW, 5PJV, 5PJU, 5PJT, 5PJS, 5PJR, 5PJQ, 5PJP, 5PJO, 5PJN, 5PJM, 5PJL, 5PJK, 5PJJ, 5PJI, 5PJH, 5PJG, 5PJF, 5PJE, 5PJD, 5PJC, 5PJB, 5PJA, 5PJ9, 5PJ8, 5PJ7, 5PJ6, 5PJ5, 5PJ4, 5PJ3, 5PJ2, 5PJ1, 5PJ0, 5PIZ, 5PIY, 5PIX, 5PIW, 5PIV, 5PIU, 5PIT, 5PIS, 5PIR, 5PIQ, 5PIP, 5PIO, 5PIN, 5PIM, 5PIL, 5PIK, 5PIJ, 5PII, 5PIH, 5PIG, 5PIF, 5PIE, 5PID, 5PIC, 5PIB, 5PIA, 5PI9, 5PI8, 5PI7, 5PI6, 5PI5, 5PI4, 5PI3, 5PI2, 5PI1, 5PI0, 5PHZ, 5PHY, 5PHX, 5PHW, 5PHV, 5PHU, 5PHT, 5PHS, 5PHR, 5PHQ, 5PHP, 5PHO, 5PHN, 5PHM, 5PHL, 5PHK, 5PHJ, 5PHI, 5PHH, 5PHG, 5PHF, 5PHD, 5PHE, 5PHC, 5PHB, 5PHA, 5PH8, 5PH9, 5PH7, 5PH6, 5PH5, 5PH3, 5PH4, 5PH2, 5PH1, 5PH0, 5PGT, 5PGS, 5PGR, 5PGQ, 5PGP, 5PGO, 5PGN, 5PGL, 5PGK, 5PGJ, 5PGI, 5PGH, 5PGG, 5PGF, 5PGE, 5PGD, 5PGC, 5PGB, 5PGA, 5PG9, 5PG8, 5PG7, 5PG6, 5PG5, 5PG4, 5PG3, 5PG2, 5PG1, 5PG0, 5PFZ, 5PFY, 5PFX, 5PFW, 5PFV, 5PFU, 5PFT, 5PFS, 5PFR, 5PFQ, 5PFP, 5PFO, 5PFN, 5PFM, 5PFL, 5PFJ, 5PFI, 5PFH, 5PFG, 5PFF, 5PFE, 5PFD, 5PFC, 5PFB, 5PFA, 5PF9, 5PF8, 5PF7, 5PF6, 5PF5, 5PF4, 5PF3, 5PF2, 5PF1, 5PF0, 5PEZ, 5PEY, 5PEX, 5PEW, 5PEV, 5PEU, 5PET, 5PES, 5PER, 5PEQ, 5PEO, 5PEN, 5PEM, 5PEL, 5PEK, 5PEJ, 5PEI, 5PEH, 5PEG, 5PEF, 5PEE, 5PED, 5PEC, 5PEB, 5PEA, 5PE9, 5PE8, 5PE7, 5PE6, 5PE5, 5PE4, 5PE3, 5PE2, 5PE1, 5PDZ, 5PE0, 5PDY, 5PDX, 5PDW, 5PDT, 5PDU, 5PDV, 5PDS, 5PDR, 5PDQ, 5PDP, 5PDO, 5PDN, 5PDM, 5PDL, 5PDK, 5PDJ, 5PDI, 5PDH, 5PDG, 5PDF, 5PDE, 5PDD, 5PDC, 5PDB, 5PDA, 5PD9, 5PD8, 5PD7, 5PD6, 5PD5, 5PD4, 5PD3, 5PD2, 5PD1, 5PD0, 5PCZ, 5PCX, 5PCW, 5PCV, 5PCU, 5PCT, 5PCS, 5PCR, 5PCQ, 5PCP, 5PCO, 5PCN, 5PCM, 5PCL, 5PCK, 5PCJ, 5PCI, 5PCH, 5PCG, 5PCF, 5PCE, 5PCD, 5PCC, 5PCB, 5PCA, 5PC9, 5PC8, 5PC7, 5PC5, 5PC6, 5PC4, 5PC3, 5PC1, 5PC2, 5PC0, 5PBZ, 5PBY, 5PBW, 5PBX, 5PBV, 5PBU, 5PBT, 5PBS, 5PBR, 5PBQ, 5PBP, 5PBO, 5PBN, 5PBM, 5PBL, 5PBK, 5PBJ, 5PBI, 5PBG, 5PBH, 5PBF, 5PBE, 5PBD, 5PBC, 5PBB, 5PBA, 5PB9, 5PB8, 5PB7


• PubMed Abstract: 
  

In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous ('weak' or 'noisy') density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state-even from inaccurate maps-by subtracting a proportion of the confounding 'ground state'; changed states are objectively identified from statistical analysis of density distributions. The method is completely general, implying new best practice for all changed-state studies, including the routine collection of multiple ground-state crystals. More generally, these results demonstrate: the incompleteness of atomic models; that single data sets contain insufficient information to model them fully; and that accuracy requires further map-deconvolution approaches.

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Organizational Affiliation: 

Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysine-specific demethylase 4D	A	364	Homo sapiens	Mutation(s): 0  Gene Names: KDM4D (JHDM3D, JMJD2D) EC: 1.14.11.-
Find proteins for Q6B0I6 (Homo sapiens) Go to Gene View: KDM4D Go to UniProtKB:  Q6B0I6

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
OGA	A	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
NI	A	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.199 
• R-Value Work: 0.179 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 71.663	α = 90.00
b = 71.663	β = 90.00
c = 150.645	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
REFMAC	refinement
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-02-07 
• Released Date: 2017-03-15 
• Deposition Author(s): Pearce, N.M., Krojer, T., Talon, R., Bradley, A.R., Fairhead, M., Sethi, R., Wright, N., MacLean, E., Collins, P., Brandao-Neto, J., Douangamath, A., Renjie, Z., Dias, A., Vollmar, M., Ng, J., Szykowska, A., Burgess-Brown, N., Brennan, P.E., Cox, O., Oppermann, U., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

Revision History 

• Version 1.0: 2017-03-15
  Type: Initial release
• Version 1.1: 2017-09-27
  Type: Advisory, Data collection, Database references, Structure summary
• Version 1.2: 2017-10-04
  Type: Structure summary