HEADER LIPID BINDING PROTEIN 02-NOV-20 7DE7 TITLE CRYSTAL STRUCTURE OF PDZD7 HHD DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PDZ DOMAIN-CONTAINING PROTEIN 7; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PDZD7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PDZD7, HHD DOMAIN, MEMBRANE-TARGETING, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,L.LIN,Q.LU REVDAT 2 29-NOV-23 7DE7 1 REMARK REVDAT 1 25-AUG-21 7DE7 0 JRNL AUTH L.LIN,H.WANG,D.REN,Y.XIA,G.HE,Q.LU JRNL TITL STRUCTURE AND MEMBRANE TARGETING OF THE PDZD7 HARMONIN JRNL TITL 2 HOMOLOGY DOMAIN (HHD) ASSOCIATED WITH HEARING LOSS. JRNL REF FRONT CELL DEV BIOL V. 9 42666 2021 JRNL REFN ESSN 2296-634X JRNL PMID 33937240 JRNL DOI 10.3389/FCELL.2021.642666 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 32580 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 37.5000 - 4.5400 1.00 2153 146 0.1890 0.2036 REMARK 3 2 4.5300 - 3.6000 1.00 2165 142 0.1442 0.1471 REMARK 3 3 3.6000 - 3.1500 1.00 2172 146 0.1644 0.1434 REMARK 3 4 3.1400 - 2.8600 1.00 2162 139 0.1675 0.1792 REMARK 3 5 2.8600 - 2.6500 1.00 2170 140 0.1586 0.1637 REMARK 3 6 2.6500 - 2.5000 1.00 2144 142 0.1570 0.1846 REMARK 3 7 2.5000 - 2.3700 1.00 2183 140 0.1478 0.1806 REMARK 3 8 2.3700 - 2.2700 1.00 2160 141 0.1653 0.1696 REMARK 3 9 2.2700 - 2.1800 1.00 2143 142 0.1473 0.2065 REMARK 3 10 2.1800 - 2.1100 1.00 2199 146 0.1582 0.1494 REMARK 3 11 2.1100 - 2.0400 1.00 2125 138 0.1540 0.2170 REMARK 3 12 2.0400 - 1.9800 1.00 2201 142 0.1658 0.1764 REMARK 3 13 1.9800 - 1.9300 1.00 2104 139 0.1623 0.1824 REMARK 3 14 1.9300 - 1.8800 1.00 2206 147 0.1870 0.1922 REMARK 3 15 1.8800 - 1.8400 1.00 2119 139 0.1838 0.2816 REMARK 3 16 1.8400 - 1.8000 0.99 2179 144 0.2024 0.2317 REMARK 3 17 1.8000 - 1.7600 1.00 2157 139 0.2025 0.2511 REMARK 3 18 1.7600 - 1.7300 1.00 2154 142 0.2124 0.2457 REMARK 3 19 1.7300 - 1.7000 1.00 2146 140 0.2200 0.2551 REMARK 3 20 1.7000 - 1.6700 0.99 2180 140 0.2275 0.2594 REMARK 3 21 1.6700 - 1.6400 0.99 2120 134 0.2396 0.2295 REMARK 3 22 1.6400 - 1.6200 0.99 2188 146 0.2552 0.2958 REMARK 3 23 1.6200 - 1.6000 1.00 2133 138 0.2552 0.3090 REMARK 3 24 1.6000 - 1.5700 0.99 2165 139 0.2803 0.2925 REMARK 3 25 1.5700 - 1.5500 0.99 2106 139 0.2929 0.3194 REMARK 3 26 1.5500 - 1.5300 0.99 2122 138 0.3047 0.3230 REMARK 3 27 1.5300 - 1.5100 0.99 2182 144 0.3438 0.3622 REMARK 3 28 1.5100 - 1.4900 0.93 1993 130 0.3535 0.4018 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7DE7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1300019233. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97891 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32592 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 37.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.740 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.44 REMARK 200 R MERGE FOR SHELL (I) : 1.19700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.560 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: 6FDD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 45% REMARK 280 POLYPROPYLENE GLYCOL P400, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K 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 37.50250 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 542 REMARK 465 PRO A 543 REMARK 465 GLY A 544 REMARK 465 SER A 545 REMARK 465 THR A 546 REMARK 465 ALA A 644 REMARK 465 VAL A 645 REMARK 465 GLY A 646 REMARK 465 GLY B 542 REMARK 465 PRO B 543 REMARK 465 GLY B 544 REMARK 465 SER B 545 REMARK 465 THR B 546 REMARK 465 LEU B 640 REMARK 465 LYS B 641 REMARK 465 SER B 642 REMARK 465 ARG B 643 REMARK 465 ALA B 644 REMARK 465 VAL B 645 REMARK 465 GLY B 646 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL A 547 CG1 CG2 REMARK 470 ARG A 643 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 547 CG1 CG2 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 884 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH B 767 DISTANCE = 6.71 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2Q5 A 701 DBREF 7DE7 A 546 646 UNP E9Q9W7 PDZD7_MOUSE 546 646 DBREF 7DE7 B 546 646 UNP E9Q9W7 PDZD7_MOUSE 546 646 SEQADV 7DE7 GLY A 542 UNP E9Q9W7 EXPRESSION TAG SEQADV 7DE7 PRO A 543 UNP E9Q9W7 EXPRESSION TAG SEQADV 7DE7 GLY A 544 UNP E9Q9W7 EXPRESSION TAG SEQADV 7DE7 SER A 545 UNP E9Q9W7 EXPRESSION TAG SEQADV 7DE7 GLY B 542 UNP E9Q9W7 EXPRESSION TAG SEQADV 7DE7 PRO B 543 UNP E9Q9W7 EXPRESSION TAG SEQADV 7DE7 GLY B 544 UNP E9Q9W7 EXPRESSION TAG SEQADV 7DE7 SER B 545 UNP E9Q9W7 EXPRESSION TAG SEQRES 1 A 105 GLY PRO GLY SER THR VAL ASN GLU GLN VAL GLN ALA TRP SEQRES 2 A 105 GLU SER ARG ARG PRO LEU ILE GLN ASP LEU ALA ARG ARG SEQRES 3 A 105 LEU LEU THR ASP ASP GLU VAL LEU ALA VAL THR ARG HIS SEQRES 4 A 105 CYS SER ARG TYR VAL HIS GLU GLY GLY VAL GLU ASP LEU SEQRES 5 A 105 VAL ARG PRO LEU LEU ALA ILE LEU ASP ARG PRO THR LYS SEQRES 6 A 105 LEU LEU LEU LEU ARG ASP ILE ARG SER VAL VAL ALA PRO SEQRES 7 A 105 THR ASP LEU GLY ARG PHE ASP SER MET VAL MET PRO VAL SEQRES 8 A 105 GLU LEU GLU ALA PHE GLU ALA LEU LYS SER ARG ALA VAL SEQRES 9 A 105 GLY SEQRES 1 B 105 GLY PRO GLY SER THR VAL ASN GLU GLN VAL GLN ALA TRP SEQRES 2 B 105 GLU SER ARG ARG PRO LEU ILE GLN ASP LEU ALA ARG ARG SEQRES 3 B 105 LEU LEU THR ASP ASP GLU VAL LEU ALA VAL THR ARG HIS SEQRES 4 B 105 CYS SER ARG TYR VAL HIS GLU GLY GLY VAL GLU ASP LEU SEQRES 5 B 105 VAL ARG PRO LEU LEU ALA ILE LEU ASP ARG PRO THR LYS SEQRES 6 B 105 LEU LEU LEU LEU ARG ASP ILE ARG SER VAL VAL ALA PRO SEQRES 7 B 105 THR ASP LEU GLY ARG PHE ASP SER MET VAL MET PRO VAL SEQRES 8 B 105 GLU LEU GLU ALA PHE GLU ALA LEU LYS SER ARG ALA VAL SEQRES 9 B 105 GLY HET 2Q5 A 701 17 HETNAM 2Q5 (2R)-2-{[(2R)-2-{[(2S)-2-{[(2R)-2- HETNAM 2 2Q5 HYDROXYPROPYL]OXY}PROPYL]OXY}PROPYL]OXY}PROPAN-1-OL FORMUL 3 2Q5 C12 H26 O5 FORMUL 4 HOH *151(H2 O) HELIX 1 AA1 VAL A 547 LEU A 569 1 23 HELIX 2 AA2 THR A 570 GLY A 588 1 19 HELIX 3 AA3 GLY A 589 LEU A 601 1 13 HELIX 4 AA4 PRO A 604 LEU A 608 5 5 HELIX 5 AA5 LEU A 609 SER A 615 1 7 HELIX 6 AA6 VAL A 616 VAL A 617 5 2 HELIX 7 AA7 ALA A 618 THR A 620 5 3 HELIX 8 AA8 ASP A 621 SER A 642 1 22 HELIX 9 AA9 ASN B 548 LEU B 569 1 22 HELIX 10 AB1 THR B 570 GLY B 588 1 19 HELIX 11 AB2 GLY B 589 LEU B 601 1 13 HELIX 12 AB3 ARG B 603 LEU B 608 1 6 HELIX 13 AB4 LEU B 608 SER B 615 1 8 HELIX 14 AB5 VAL B 616 VAL B 617 5 2 HELIX 15 AB6 ALA B 618 THR B 620 5 3 HELIX 16 AB7 ASP B 621 ALA B 639 1 19 SITE 1 AC1 8 LEU A 607 ARG A 611 GLU A 633 HOH A 835 SITE 2 AC1 8 LEU B 610 ARG B 611 PHE B 625 GLU B 633 CRYST1 32.782 75.005 42.939 90.00 103.10 90.00 P 1 21 1 4 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 0.030505 0.000000 0.007100 0.00000 SCALE2 0.000000 0.013332 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023911 0.00000