HEADER DNA BINDING PROTEIN/DNA 28-FEB-23 8IK5 TITLE TRANSCRIPTION FACTOR LMX1A HOMEOBOX DOMAIN IN COMPLEX WITH WNT1 TITLE 2 PROMOTER COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*AP*TP*AP*TP*TP*TP*AP*AP*TP*CP*TP*TP*C)- COMPND 3 3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*GP*AP*AP*GP*AP*TP*TP*AP*AP*AP*TP*AP*TP*G)- COMPND 8 3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: LMX1A FACTOR; COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: SEQUENCE REFERENCE FOR HOMO SAPIENS IS NOT AVAILABLE COMPND 16 IN UNIPROT AT THE TIME OF BIOCURATION. CURRENT SEQUENCE REFERENCE IS COMPND 17 FROM UNIPROT ID A0A7K7QDL0. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-DSDNA COMPLEX, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.Q.LV,L.Q.LIN REVDAT 1 06-MAR-24 8IK5 0 JRNL AUTH M.Q.LV,L.Q.LIN JRNL TITL STRUCTURAL INSIGHTS INTO THE RECOGNITION OF THE A/T-RICH JRNL TITL 2 MOTIF IN TARGET GENE PROMOTERS BY THE LMX1A HOMEOBOX DOMAIN JRNL REF FEBS J. 2024 JRNL REFN ISSN 1742-464X REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 3.3.22 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 14659 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 707 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 27.0770 - 3.3993 0.99 2941 151 0.1761 0.1963 REMARK 3 2 3.3993 - 2.6989 0.99 2794 144 0.2320 0.2510 REMARK 3 3 2.6989 - 2.3579 1.00 2782 139 0.2471 0.3021 REMARK 3 4 2.3579 - 2.1425 1.00 2771 133 0.2376 0.3005 REMARK 3 5 2.1425 - 1.9890 0.97 2664 140 0.2616 0.3224 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 1233 REMARK 3 ANGLE : 0.952 1785 REMARK 3 CHIRALITY : 0.043 200 REMARK 3 PLANARITY : 0.005 122 REMARK 3 DIHEDRAL : 24.415 637 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 1 THROUGH 15) REMARK 3 ORIGIN FOR THE GROUP (A): 8.4896 1.7893 26.4771 REMARK 3 T TENSOR REMARK 3 T11: 0.3489 T22: 0.5578 REMARK 3 T33: 0.3742 T12: 0.0492 REMARK 3 T13: 0.0023 T23: 0.0330 REMARK 3 L TENSOR REMARK 3 L11: 4.6054 L22: 5.9212 REMARK 3 L33: 7.8895 L12: -0.7931 REMARK 3 L13: 0.7393 L23: -0.1658 REMARK 3 S TENSOR REMARK 3 S11: 0.2410 S12: -0.2628 S13: 0.0654 REMARK 3 S21: 0.1530 S22: 0.2350 S23: 0.7124 REMARK 3 S31: -0.2400 S32: -1.5128 S33: -0.3653 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 15) REMARK 3 ORIGIN FOR THE GROUP (A): 9.2975 -0.6030 22.7996 REMARK 3 T TENSOR REMARK 3 T11: 0.3560 T22: 0.5283 REMARK 3 T33: 0.3133 T12: 0.0313 REMARK 3 T13: -0.0282 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 5.1667 L22: 5.4248 REMARK 3 L33: 6.7879 L12: -0.1793 REMARK 3 L13: -0.3516 L23: -1.1334 REMARK 3 S TENSOR REMARK 3 S11: 0.2526 S12: 0.2194 S13: -0.0934 REMARK 3 S21: -0.2967 S22: 0.1525 S23: 0.5261 REMARK 3 S31: -0.1496 S32: -1.5371 S33: -0.3226 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 190 THROUGH 256) REMARK 3 ORIGIN FOR THE GROUP (A): 19.8454 -1.1630 19.8356 REMARK 3 T TENSOR REMARK 3 T11: 0.2543 T22: 0.3288 REMARK 3 T33: 0.1941 T12: 0.0310 REMARK 3 T13: 0.0312 T23: -0.0253 REMARK 3 L TENSOR REMARK 3 L11: 3.9082 L22: 7.7134 REMARK 3 L33: 3.8750 L12: -0.3470 REMARK 3 L13: 0.4080 L23: 0.1912 REMARK 3 S TENSOR REMARK 3 S11: 0.0774 S12: 0.4636 S13: -0.0833 REMARK 3 S21: -0.4048 S22: -0.2153 S23: -0.0034 REMARK 3 S31: -0.0502 S32: -0.2580 S33: 0.0860 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 8IK5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 10-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1300035847. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14659 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.989 REMARK 200 RESOLUTION RANGE LOW (A) : 27.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.60700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG MME 2000, 0.1 MM SODIUM REMARK 280 CACODYLATE (PH 6.5), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.14500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.04900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.20950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.04900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.14500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.20950 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 LYS C 193 CG CD CE NZ REMARK 470 ARG C 194 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 197 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 223 CG CD CE NZ REMARK 470 ARG C 256 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DA B 4 O3' DA B 4 C3' -0.041 REMARK 500 REMARK 500 REMARK: NULL DBREF 8IK5 A 1 15 PDB 8IK5 8IK5 1 15 DBREF 8IK5 B 1 15 PDB 8IK5 8IK5 1 15 DBREF1 8IK5 C 192 256 UNP A0A7K7QDL0_POEAT DBREF2 8IK5 C A0A7K7QDL0 191 255 SEQADV 8IK5 HIS C 190 UNP A0A7K7QDL EXPRESSION TAG SEQADV 8IK5 MET C 191 UNP A0A7K7QDL EXPRESSION TAG SEQRES 1 A 15 DC DC DA DT DA DT DT DT DA DA DT DC DT SEQRES 2 A 15 DT DC SEQRES 1 B 15 DG DG DA DA DG DA DT DT DA DA DA DT DA SEQRES 2 B 15 DT DG SEQRES 1 C 67 HIS MET HIS LYS ARG PRO LYS ARG PRO ARG THR ILE LEU SEQRES 2 C 67 THR THR GLN GLN ARG ARG ALA PHE LYS ALA SER PHE GLU SEQRES 3 C 67 VAL SER SER LYS PRO CYS ARG LYS VAL ARG GLU THR LEU SEQRES 4 C 67 ALA ALA GLU THR GLY LEU SER VAL ARG VAL VAL GLN VAL SEQRES 5 C 67 TRP PHE GLN ASN GLN ARG ALA LYS MET LYS LYS LEU ALA SEQRES 6 C 67 ARG ARG HET GOL C 301 6 HET GOL C 302 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 HOH *71(H2 O) HELIX 1 AA1 THR C 203 SER C 217 1 15 HELIX 2 AA2 CYS C 221 GLY C 233 1 13 HELIX 3 AA3 SER C 235 ALA C 254 1 20 CRYST1 46.290 46.419 96.098 90.00 90.00 90.00 P 21 21 21 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 0.021603 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021543 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010406 0.00000