HEADER MEMBRANE PROTEIN 22-JUN-21 7OXE TITLE CRYSTAL STRUCTURE OF THE KDEL RECEPTOR BOUND TO HDEF PEPTIDE AT PH 6.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ER LUMEN PROTEIN-RETAINING RECEPTOR 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: KDEL ENDOPLASMIC RETICULUM PROTEIN RETENTION RECEPTOR 2,KDEL COMPND 5 RECEPTOR 2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: THR-ALA-GLU-HIS-ASP-GLU-PHE; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: PEPTIDE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: KDELR2, RCJMB04_8L23; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BJ5460; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS TRAFFICKING RECEPTOR, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.NEWSTEAD,J.L.PARKER REVDAT 4 13-NOV-24 7OXE 1 REMARK REVDAT 3 04-SEP-24 7OXE 1 JRNL REVDAT 2 31-JAN-24 7OXE 1 REMARK REVDAT 1 13-JUL-22 7OXE 0 JRNL AUTH Z.WU,K.SMITH,A.GERONDOPOULOS,T.SOBAJIMA,J.L.PARKER,F.A.BARR, JRNL AUTH 2 S.NEWSTEAD,P.C.BIGGIN JRNL TITL MOLECULAR BASIS FOR PH SENSING IN THE KDEL TRAFFICKING JRNL TITL 2 RECEPTOR. JRNL REF STRUCTURE V. 32 866 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 38626766 JRNL DOI 10.1016/J.STR.2024.03.013 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.4 (20-APR-2021) REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 10122 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.245 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 503 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.31 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.79 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 382 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.68 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 23 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1775 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 100 REMARK 3 SOLVENT ATOMS : 51 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.14350 REMARK 3 B22 (A**2) : -0.11560 REMARK 3 B33 (A**2) : -4.02790 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.52380 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.380 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.488 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.281 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.584 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.287 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.908 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.859 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2081 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2958 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 691 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 310 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1921 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 242 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1618 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 0.85 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.79 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.94 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS WERE FULLY REFINED WITH ZERO REMARK 3 OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REMARK 3 REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT REMARK 3 SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY REMARK 4 REMARK 4 7OXE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1292116585. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10122 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.283 REMARK 200 RESOLUTION RANGE LOW (A) : 62.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6ZXR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 600, 0.1M MES PH 6.0, 0.1M REMARK 280 SODIUM NITRATE, LIPIDIC CUBIC PHASE, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 18.76650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PRO A 211 REMARK 465 ALA A 212 REMARK 465 THR B 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 201 -66.37 -107.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 7OXE A 1 212 UNP Q5ZKX9 ERD22_CHICK 1 212 DBREF 7OXE B 1 7 PDB 7OXE 7OXE 1 7 SEQRES 1 A 212 MET ASN ILE PHE ARG LEU THR GLY ASP LEU SER HIS LEU SEQRES 2 A 212 ALA ALA ILE ILE ILE LEU LEU LEU LYS ILE TRP LYS SER SEQRES 3 A 212 ARG SER CYS ALA GLY ILE SER GLY LYS SER GLN LEU LEU SEQRES 4 A 212 PHE ALA LEU VAL PHE THR THR ARG TYR LEU ASP LEU PHE SEQRES 5 A 212 THR SER PHE ILE SER LEU TYR ASN THR SER MET LYS LEU SEQRES 6 A 212 ILE TYR ILE ALA CYS SER TYR ALA THR VAL TYR LEU ILE SEQRES 7 A 212 TYR MET LYS PHE LYS ALA THR TYR ASP GLY ASN HIS ASP SEQRES 8 A 212 THR PHE ARG VAL GLU PHE LEU ILE VAL PRO VAL GLY GLY SEQRES 9 A 212 LEU SER PHE LEU VAL ASN HIS ASP PHE SER PRO LEU GLU SEQRES 10 A 212 ILE LEU TRP THR PHE SER ILE TYR LEU GLU SER VAL ALA SEQRES 11 A 212 ILE LEU PRO GLN LEU PHE MET ILE SER LYS THR GLY GLU SEQRES 12 A 212 ALA GLU THR ILE THR THR HIS TYR LEU PHE PHE LEU GLY SEQRES 13 A 212 LEU TYR ARG ALA LEU TYR LEU VAL ASN TRP ILE TRP ARG SEQRES 14 A 212 TYR TYR PHE GLU GLY PHE PHE ASP LEU ILE ALA VAL VAL SEQRES 15 A 212 ALA GLY VAL VAL GLN THR VAL LEU TYR CYS ASP PHE PHE SEQRES 16 A 212 TYR LEU TYR VAL THR LYS VAL LEU LYS GLY LYS LYS LEU SEQRES 17 A 212 SER LEU PRO ALA SEQRES 1 B 7 THR ALA GLU HIS ASP GLU PHE HET OLC A 301 65 HET OLC A 302 65 HET OLC A 303 65 HET OLC A 304 65 HETNAM OLC (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE HETSYN OLC 1-OLEOYL-R-GLYCEROL FORMUL 3 OLC 4(C21 H40 O4) FORMUL 7 HOH *51(H2 O) HELIX 1 AA1 ASN A 2 ARG A 27 1 26 HELIX 2 AA2 SER A 33 TYR A 48 1 16 HELIX 3 AA3 LEU A 49 THR A 53 5 5 HELIX 4 AA4 SER A 57 MET A 80 1 24 HELIX 5 AA5 PHE A 82 TYR A 86 5 5 HELIX 6 AA6 VAL A 95 VAL A 109 1 15 HELIX 7 AA7 SER A 114 ALA A 130 1 17 HELIX 8 AA8 ILE A 131 GLY A 142 1 12 HELIX 9 AA9 GLU A 145 GLY A 174 1 30 HELIX 10 AB1 ASP A 177 LEU A 190 1 14 HELIX 11 AB2 TYR A 191 LYS A 201 1 11 HELIX 12 AB3 VAL A 202 GLY A 205 5 4 CRYST1 47.383 37.533 62.685 90.00 95.22 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021105 0.000000 0.001928 0.00000 SCALE2 0.000000 0.026643 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016019 0.00000