HEADER PROTEIN BINDING 18-JAN-24 8VQP TITLE CRYSTAL STRUCTURE ANALYSIS OF EGR1-MIDN COMPND MOL_ID: 1; COMPND 2 MOLECULE: EGR1-MIDN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS UBIQUITIN-INDEPENDENT PROTEASOMAL DEGRADATION, PEPTIDE BINDING, KEYWDS 2 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR H.-S.SEO,S.DHE-PAGANON REVDAT 1 23-JUL-25 8VQP 0 JRNL AUTH H.-S.SEO,S.DHE-PAGANON JRNL TITL CRYSTAL STRUCTURE ANALYSIS OF EGR1-MIDN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 5208 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 251 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 42.3900 - 3.1800 1.00 2532 125 0.2324 0.2544 REMARK 3 2 3.1700 - 2.5200 1.00 2425 126 0.3105 0.3611 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.510 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 NULL REMARK 3 ANGLE : 1.193 NULL REMARK 3 CHIRALITY : 0.065 144 REMARK 3 PLANARITY : 0.009 163 REMARK 3 DIHEDRAL : 6.714 124 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 5.8983 -1.5242 9.3177 REMARK 3 T TENSOR REMARK 3 T11: 0.8413 T22: 0.8382 REMARK 3 T33: 0.8656 T12: -0.0266 REMARK 3 T13: -0.0274 T23: -0.0550 REMARK 3 L TENSOR REMARK 3 L11: 4.4450 L22: 5.9218 REMARK 3 L33: 6.5755 L12: -0.0968 REMARK 3 L13: -2.6383 L23: 1.8000 REMARK 3 S TENSOR REMARK 3 S11: 0.2702 S12: -0.4675 S13: 0.5393 REMARK 3 S21: 0.7436 S22: -0.0484 S23: -0.2477 REMARK 3 S31: -0.9019 S32: 0.1150 S33: -0.0058 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 8VQP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1000279472. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-23 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 : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5217 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.520 REMARK 200 RESOLUTION RANGE LOW (A) : 42.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 2.39200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES, PH 7.0 1.4M NH4SO4, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 24.73000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.39000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.03000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.39000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.73000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.03000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 24.73000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.03000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.39000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.03000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.73000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.39000 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: 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 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 1 REMARK 465 PRO A 2 REMARK 465 GLY A 3 REMARK 465 ASN A 20 REMARK 465 SER A 21 REMARK 465 GLY A 22 REMARK 465 ASN A 23 REMARK 465 THR A 24 REMARK 465 LEU A 25 REMARK 465 SER A 26 REMARK 465 ARG A 27 REMARK 465 PRO A 28 REMARK 465 GLU A 29 REMARK 465 ALA A 73 REMARK 465 GLN A 74 REMARK 465 HIS A 75 REMARK 465 ALA A 76 REMARK 465 PRO A 77 REMARK 465 PRO A 78 REMARK 465 ALA A 79 REMARK 465 PRO A 80 REMARK 465 ARG A 81 REMARK 465 SER A 82 REMARK 465 ARG A 83 REMARK 465 PRO A 144 REMARK 465 PRO A 145 REMARK 465 SER A 146 REMARK 465 LEU A 147 REMARK 465 ALA A 148 REMARK 465 GLN A 149 REMARK 465 LEU A 150 REMARK 465 ARG A 151 REMARK 465 CYS A 152 REMARK 465 HIS A 153 REMARK 465 ALA A 154 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 TYR A 140 CG CD1 CD2 CE1 CE2 CZ OH DBREF 8VQP A 1 154 PDB 8VQP 8VQP 1 154 SEQRES 1 A 154 GLY PRO GLY SER PRO PRO ILE THR TYR THR GLY ARG PHE SEQRES 2 A 154 SER LEU GLU PRO ALA PRO ASN SER GLY ASN THR LEU SER SEQRES 3 A 154 ARG PRO GLU GLN SER VAL MET GLN ALA LEU GLU SER LEU SEQRES 4 A 154 THR GLU THR GLN VAL SER ASP PHE LEU SER GLY ARG SER SEQRES 5 A 154 PRO LEU THR LEU ALA LEU ARG VAL GLY ASP HIS MET MET SEQRES 6 A 154 PHE VAL GLN LEU GLN LEU ALA ALA GLN HIS ALA PRO PRO SEQRES 7 A 154 ALA PRO ARG SER ARG LYS PRO GLY ALA VAL ILE GLU SER SEQRES 8 A 154 PHE VAL ASN HIS ALA PRO GLY VAL PHE SER GLY THR PHE SEQRES 9 A 154 SER GLY THR LEU HIS PRO ASN CYS GLN ASP SER SER GLY SEQRES 10 A 154 ARG PRO ARG ARG ASP ILE GLY THR ILE LEU GLN ILE LEU SEQRES 11 A 154 ASN ASP LEU LEU SER ALA THR ARG HIS TYR GLN GLY MET SEQRES 12 A 154 PRO PRO SER LEU ALA GLN LEU ARG CYS HIS ALA FORMUL 2 HOH *(H2 O) HELIX 1 AA1 SER A 31 LEU A 39 1 9 HELIX 2 AA2 THR A 40 GLY A 50 1 11 HELIX 3 AA3 HIS A 109 GLN A 113 5 5 HELIX 4 AA4 ASP A 122 ARG A 138 1 17 SHEET 1 AA1 5 LEU A 54 VAL A 60 0 SHEET 2 AA1 5 HIS A 63 LEU A 71 -1 O LEU A 69 N LEU A 54 SHEET 3 AA1 5 THR A 8 PRO A 17 -1 N THR A 10 O GLN A 70 SHEET 4 AA1 5 VAL A 99 THR A 107 -1 O GLY A 102 N PHE A 13 SHEET 5 AA1 5 GLY A 86 ALA A 96 -1 N ALA A 96 O VAL A 99 CRYST1 49.460 70.060 84.780 90.00 90.00 90.00 I 21 21 21 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 0.020218 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014273 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011795 0.00000 MASTER 268 0 0 4 5 0 0 6 900 1 0 12 END