HEADER MEMBRANE PROTEIN 24-JUN-21 7OYE TITLE CRYSTAL STRUCTURE OF THE KDEL RECEPTOR BOUND TO HDEL PEPTIDE AT PH 7.0 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-LEU; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES 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_TAXID: 9606 KEYWDS TRAFFICKING RECEPTOR, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.NEWSTEAD,P.BRAEUER REVDAT 2 31-JAN-24 7OYE 1 REMARK REVDAT 1 13-JUL-22 7OYE 0 JRNL AUTH S.NEWSTEAD,P.BRAEUER JRNL TITL CRYSTAL STRUCTURE OF THE KDEL RECEPTOR BOUND TO HDEL PEPTIDE JRNL TITL 2 AT PH 7.0 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.62 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) : 2.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 6853 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) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 347 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 : 18 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.62 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.67 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.79 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 404 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.3175 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 385 REMARK 3 BIN R VALUE (WORKING SET) : 0.3124 REMARK 3 BIN FREE R VALUE : 0.4388 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 19 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 : 1764 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 128 REMARK 3 SOLVENT ATOMS : 62 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 64.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.24840 REMARK 3 B22 (A**2) : -6.05620 REMARK 3 B33 (A**2) : 16.30460 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -7.82700 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.350 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.381 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL 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 : 0.905 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1935 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2588 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 696 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 303 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1935 ; 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 : 1415 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 0.88 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.61 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.89 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { *|* } REMARK 3 ORIGIN FOR THE GROUP (A): 45.1961 38.2938 79.9976 REMARK 3 T TENSOR REMARK 3 T11: -0.2737 T22: -0.1130 REMARK 3 T33: 0.2163 T12: -0.0214 REMARK 3 T13: 0.1014 T23: -0.0210 REMARK 3 L TENSOR REMARK 3 L11: 1.8309 L22: 2.6843 REMARK 3 L33: 2.6073 L12: -0.0954 REMARK 3 L13: -0.5857 L23: -0.5603 REMARK 3 S TENSOR REMARK 3 S11: 0.0115 S12: 0.2241 S13: 0.1218 REMARK 3 S21: -0.0395 S22: -0.0182 S23: -0.0889 REMARK 3 S31: -0.0587 S32: -0.0238 S33: 0.0067 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7OYE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1292116605. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.9698 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6860 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.620 REMARK 200 RESOLUTION RANGE LOW (A) : 38.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.14900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.99700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 6I6H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 500DME 100MM HEPES PH 7.0 REMARK 280 100MM POTASSIUM THIOCYANATE, LIPIDIC CUBIC PHASE, TEMPERATURE REMARK 280 298K 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 19.01500 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: 1270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 LEU A 210 REMARK 465 PRO A 211 REMARK 465 ALA A 212 REMARK 465 THR B 2 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 MET A 80 -65.53 -125.94 REMARK 500 LYS A 201 -65.81 -106.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 457 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 458 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A 459 DISTANCE = 7.56 ANGSTROMS DBREF 7OYE A 1 212 UNP Q5ZKX9 ERD22_CHICK 1 212 DBREF 7OYE B 2 8 PDB 7OYE 7OYE 2 8 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 LEU HET OLC A 301 25 HET OLC A 302 25 HET OLC A 303 25 HET OLC A 304 25 HET OLC A 305 25 HET CO2 B 901 3 HETNAM OLC (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE HETNAM CO2 CARBON DIOXIDE HETSYN OLC 1-OLEOYL-R-GLYCEROL FORMUL 3 OLC 5(C21 H40 O4) FORMUL 8 CO2 C O2 FORMUL 9 HOH *62(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 48.020 38.030 62.510 90.00 95.42 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 0.020825 0.000000 0.001976 0.00000 SCALE2 0.000000 0.026295 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016069 0.00000