HEADER PROTEIN BINDING 09-JUL-22 7YFU TITLE STRUCTURE OF RPGRIP1L CC2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN FANTOM; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NEPHROCYSTIN-8,RPGR-INTERACTING PROTEIN 1-LIKE PROTEIN, COMPND 5 RPGRIP1-LIKE PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RPGRIP1L, FTM, NPHP8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURAL PROTEIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR R.HE,G.CHEN,Z.LI,J.LI REVDAT 2 29-MAY-24 7YFU 1 REMARK REVDAT 1 17-MAY-23 7YFU 0 JRNL AUTH R.HE,G.CHEN,Z.LI,J.LI JRNL TITL STRUCTURE OF THE N-TERMINAL COILED-COIL DOMAINS OF THE JRNL TITL 2 CILIARY PROTEIN RPGRIP1L. JRNL REF ISCIENCE V. 26 06249 2023 JRNL REFN ESSN 2589-0042 JRNL PMID 36915689 JRNL DOI 10.1016/J.ISCI.2023.106249 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 13120 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 628 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 21.1600 - 2.3800 1.00 3237 167 0.1681 0.2139 REMARK 3 2 2.3800 - 1.8900 1.00 3166 159 0.1898 0.2212 REMARK 3 3 1.8900 - 1.6500 1.00 3129 157 0.1953 0.2237 REMARK 3 4 1.6500 - 1.5000 0.94 2960 145 0.1771 0.1957 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.97 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 : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -3 THROUGH 2 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.1685 -6.5514 16.8905 REMARK 3 T TENSOR REMARK 3 T11: 0.2637 T22: 0.3555 REMARK 3 T33: 0.3154 T12: 0.0070 REMARK 3 T13: 0.0053 T23: -0.0590 REMARK 3 L TENSOR REMARK 3 L11: 8.3021 L22: 4.1005 REMARK 3 L33: 3.9360 L12: -4.5735 REMARK 3 L13: -5.2065 L23: 3.6172 REMARK 3 S TENSOR REMARK 3 S11: -0.8194 S12: -0.0606 S13: -0.9059 REMARK 3 S21: 0.2048 S22: -0.0197 S23: 1.0203 REMARK 3 S31: 0.0417 S32: -1.0668 S33: 0.6781 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.9313 0.0710 10.0186 REMARK 3 T TENSOR REMARK 3 T11: 0.1690 T22: 0.1313 REMARK 3 T33: 0.1711 T12: -0.0118 REMARK 3 T13: 0.0064 T23: -0.0161 REMARK 3 L TENSOR REMARK 3 L11: 5.1319 L22: 0.6853 REMARK 3 L33: 0.6787 L12: 2.7982 REMARK 3 L13: -1.4913 L23: -1.0110 REMARK 3 S TENSOR REMARK 3 S11: 0.0269 S12: 0.1313 S13: 0.2864 REMARK 3 S21: 0.0382 S22: 0.0095 S23: 0.1484 REMARK 3 S31: -0.0598 S32: 0.0158 S33: -0.0989 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID -3 THROUGH 2 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.5766 -22.9543 7.0527 REMARK 3 T TENSOR REMARK 3 T11: 0.4809 T22: 0.2191 REMARK 3 T33: 0.2865 T12: -0.0082 REMARK 3 T13: 0.0500 T23: 0.0468 REMARK 3 L TENSOR REMARK 3 L11: 7.9159 L22: 2.3307 REMARK 3 L33: 1.8863 L12: 1.6345 REMARK 3 L13: -1.1135 L23: 1.1548 REMARK 3 S TENSOR REMARK 3 S11: -0.4267 S12: -0.2500 S13: -0.9694 REMARK 3 S21: -0.0022 S22: 0.3897 S23: -0.3286 REMARK 3 S31: 1.2557 S32: -0.0376 S33: -0.0078 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 3 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.1432 -9.1074 8.3662 REMARK 3 T TENSOR REMARK 3 T11: 0.1877 T22: 0.1444 REMARK 3 T33: 0.1547 T12: -0.0393 REMARK 3 T13: -0.0005 T23: -0.0246 REMARK 3 L TENSOR REMARK 3 L11: 6.2851 L22: 0.5631 REMARK 3 L33: 0.6423 L12: 2.6632 REMARK 3 L13: 1.6626 L23: 0.6252 REMARK 3 S TENSOR REMARK 3 S11: -0.1081 S12: 0.1891 S13: -0.3152 REMARK 3 S21: -0.0402 S22: 0.0878 S23: -0.0825 REMARK 3 S31: 0.0387 S32: -0.0207 S33: -0.0051 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 7YFU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030834. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-21 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 : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13124 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.33600 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: AB INITIO PHASING REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.81000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.46950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.81000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.46950 REMARK 290 SMTRY3 4 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: 1290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 GLY A 41 REMARK 465 GLY B 41 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 GLN A 40 CG CD OE1 NE2 REMARK 470 GLN B 40 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 136 O HOH A 147 2.01 REMARK 500 O PRO B -2 O HOH B 101 2.02 REMARK 500 OE2 GLU B 7 O HOH B 102 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 133 O HOH B 121 2556 2.14 REMARK 500 REMARK 500 REMARK: NULL DBREF 7YFU A 1 41 UNP Q8CG73 FTM_MOUSE 104 144 DBREF 7YFU B 1 41 UNP Q8CG73 FTM_MOUSE 104 144 SEQADV 7YFU GLY A -3 UNP Q8CG73 EXPRESSION TAG SEQADV 7YFU PRO A -2 UNP Q8CG73 EXPRESSION TAG SEQADV 7YFU GLY A -1 UNP Q8CG73 EXPRESSION TAG SEQADV 7YFU SER A 0 UNP Q8CG73 EXPRESSION TAG SEQADV 7YFU GLY B -3 UNP Q8CG73 EXPRESSION TAG SEQADV 7YFU PRO B -2 UNP Q8CG73 EXPRESSION TAG SEQADV 7YFU GLY B -1 UNP Q8CG73 EXPRESSION TAG SEQADV 7YFU SER B 0 UNP Q8CG73 EXPRESSION TAG SEQRES 1 A 45 GLY PRO GLY SER ARG ASP VAL GLU MET GLU GLU MET ILE SEQRES 2 A 45 GLU GLN LEU GLN GLU LYS VAL HIS GLU LEU GLU ARG GLN SEQRES 3 A 45 ASN GLU VAL LEU LYS ASN ARG LEU ILE SER ALA LYS GLN SEQRES 4 A 45 GLN LEU GLN VAL GLN GLY SEQRES 1 B 45 GLY PRO GLY SER ARG ASP VAL GLU MET GLU GLU MET ILE SEQRES 2 B 45 GLU GLN LEU GLN GLU LYS VAL HIS GLU LEU GLU ARG GLN SEQRES 3 B 45 ASN GLU VAL LEU LYS ASN ARG LEU ILE SER ALA LYS GLN SEQRES 4 B 45 GLN LEU GLN VAL GLN GLY FORMUL 3 HOH *112(H2 O) HELIX 1 AA1 ASP A 2 VAL A 39 1 38 HELIX 2 AA2 ASP B 2 GLN B 38 1 37 CRYST1 81.620 26.939 37.469 90.00 90.69 90.00 C 1 2 1 8 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 0.012252 0.000000 0.000148 0.00000 SCALE2 0.000000 0.037121 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026691 0.00000