HEADER DE NOVO PROTEIN 25-FEB-16 5IEP TITLE STRUCTURE OF CDL2.3B, A COMPUTATIONALLY DESIGNED VITAMIN-D3 BINDER COMPND MOL_ID: 1; COMPND 2 MOLECULE: CDL2.3B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: COMPUTATIONAL DESIGN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ROSSETTA, LIGAND BINDER, COMPUTATIONAL, STRUCTURAL GENOMICS, DE NOVO KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.L.STODDARD,L.A.DOYLE REVDAT 6 27-SEP-23 5IEP 1 REMARK REVDAT 5 12-FEB-20 5IEP 1 JRNL REVDAT 4 25-DEC-19 5IEP 1 REMARK REVDAT 3 18-JUL-18 5IEP 1 TITLE COMPND JRNL REVDAT 2 27-SEP-17 5IEP 1 REMARK REVDAT 1 01-MAR-17 5IEP 0 JRNL AUTH A.L.DAY,P.GREISEN,L.DOYLE,A.SCHENA,N.STELLA,K.JOHNSSON, JRNL AUTH 2 D.BAKER,B.STODDARD JRNL TITL UNINTENDED SPECIFICITY OF AN ENGINEERED LIGAND-BINDING JRNL TITL 2 PROTEIN FACILITATED BY UNPREDICTED PLASTICITY OF THE PROTEIN JRNL TITL 3 FOLD. JRNL REF PROTEIN ENG.DES.SEL. V. 31 375 2018 JRNL REFN ESSN 1741-0134 JRNL PMID 30566669 JRNL DOI 10.1093/PROTEIN/GZY031 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 13049 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1305 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 32.1360 - 3.9363 0.99 1422 157 0.2112 0.2077 REMARK 3 2 3.9363 - 3.1252 1.00 1334 149 0.2300 0.2139 REMARK 3 3 3.1252 - 2.7304 1.00 1322 147 0.2317 0.3001 REMARK 3 4 2.7304 - 2.4809 1.00 1304 144 0.2350 0.2884 REMARK 3 5 2.4809 - 2.3031 1.00 1310 146 0.2338 0.2825 REMARK 3 6 2.3031 - 2.1674 0.98 1263 141 0.2431 0.2633 REMARK 3 7 2.1674 - 2.0588 1.00 1296 144 0.2363 0.2613 REMARK 3 8 2.0588 - 1.9692 1.00 1291 144 0.2501 0.3628 REMARK 3 9 1.9692 - 1.8934 0.94 1202 133 0.2851 0.3192 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.91 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 : 0.003 939 REMARK 3 ANGLE : 0.826 1279 REMARK 3 CHIRALITY : 0.037 140 REMARK 3 PLANARITY : 0.004 161 REMARK 3 DIHEDRAL : 11.937 322 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 5IEP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13126 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.24200 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 2.5.6 REMARK 200 STARTING MODEL: 3HX8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, 0.1 M SODIUM REMARK 280 CACODYLATE PH 6.5, 32% PEG8000, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.39350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.92400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.92400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.19675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.92400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.92400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.59025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.92400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.92400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 15.19675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.92400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.92400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.59025 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 30.39350 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 348 LIES ON A SPECIAL POSITION. 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 ASP A 1 REMARK 465 GLY A 92 REMARK 465 LYS A 93 REMARK 465 ASP A 94 REMARK 465 SER A 95 REMARK 465 LYS A 96 REMARK 465 ALA A 128 REMARK 465 LYS A 129 REMARK 465 LEU A 130 REMARK 465 GLU A 131 REMARK 465 HIS A 132 REMARK 465 HIS A 133 REMARK 465 HIS A 134 REMARK 465 HIS A 135 REMARK 465 HIS A 136 REMARK 465 HIS A 137 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 A 17 CD CE NZ REMARK 470 LYS A 22 CD CE NZ REMARK 470 LEU A 40 CD1 CD2 REMARK 470 GLN A 49 CG CD OE1 NE2 REMARK 470 LYS A 53 CD CE NZ REMARK 470 LYS A 67 CD CE NZ REMARK 470 ASN A 72 CG OD1 ND2 REMARK 470 GLN A 74 OE1 NE2 REMARK 470 LYS A 75 NZ REMARK 470 LYS A 89 CE NZ REMARK 470 LEU A 97 CG CD1 CD2 REMARK 470 ARG A 109 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 110 CD CE NZ REMARK 470 GLN A 112 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 OD1 ASP A 14 HZ2 LYS A 30 1.22 REMARK 500 OD1 ASP A 14 NZ LYS A 30 1.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue VDY A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5IEN RELATED DB: PDB REMARK 900 RELATED ID: 5IEO RELATED DB: PDB REMARK 900 RELATED ID: 5IER RELATED DB: PDB REMARK 900 RELATED ID: 5IF6 RELATED DB: PDB DBREF 5IEP A 1 137 PDB 5IEP 5IEP 1 137 SEQRES 1 A 137 ASP GLN SER ALA LYS GLU ALA ILE GLU ALA ALA LEU ALA SEQRES 2 A 137 ASP PHE VAL LYS VAL TYR ASN SER LYS ASP ALA ALA GLY SEQRES 3 A 137 VAL ALA SER LYS TYR MET ASP ASP ALA ALA ILE PHE PRO SEQRES 4 A 137 LEU ASP MET ALA PRO VAL ASP GLY ARG GLN ASN ILE GLN SEQRES 5 A 137 LYS LEU TRP GLN GLY LEU MET ASP MET GLY VAL SER GLU SEQRES 6 A 137 PRO LYS PHE THR THR LEU ASN VAL GLN LYS SER GLY ASP SEQRES 7 A 137 PHE ALA PHE GLU SER GLY SER PHE SER LEU LYS GLY PRO SEQRES 8 A 137 GLY LYS ASP SER LYS LEU VAL ASP ILE ALA GLY ILE TYR SEQRES 9 A 137 VAL GLU VAL TRP ARG LYS GLY GLN ASP GLY GLY TRP LYS SEQRES 10 A 137 LEU TYR ARG THR ILE ALA ASN LEU ASP PRO ALA LYS LEU SEQRES 11 A 137 GLU HIS HIS HIS HIS HIS HIS HET VDY A 201 73 HETNAM VDY 3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL- HETNAM 2 VDY OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE- HETNAM 3 VDY CYCLOHEXANOL HETSYN VDY 25-HYDROXYVITAMIN D3 FORMUL 2 VDY C27 H44 O2 FORMUL 3 HOH *60(H2 O) HELIX 1 AA1 SER A 3 SER A 21 1 19 HELIX 2 AA2 ASP A 23 SER A 29 1 7 HELIX 3 AA3 GLY A 47 MET A 61 1 15 SHEET 1 AA1 6 VAL A 45 ASP A 46 0 SHEET 2 AA1 6 TYR A 31 PRO A 39 -1 N ILE A 37 O VAL A 45 SHEET 3 AA1 6 TRP A 116 LEU A 125 1 O LEU A 118 N MET A 32 SHEET 4 AA1 6 VAL A 98 LYS A 110 -1 N ARG A 109 O LYS A 117 SHEET 5 AA1 6 PHE A 79 GLY A 90 -1 N GLY A 90 O VAL A 98 SHEET 6 AA1 6 SER A 64 SER A 76 -1 N GLN A 74 O PHE A 81 SITE 1 AC1 7 PHE A 15 PHE A 86 LEU A 88 ILE A 100 SITE 2 AC1 7 TYR A 104 GLU A 106 HOH A 312 CRYST1 71.848 71.848 60.787 90.00 90.00 90.00 P 41 21 2 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 0.013918 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013918 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016451 0.00000