HEADER DE NOVO PROTEIN 28-AUG-23 8W6F TITLE APO STRUCTURE OF HBC BINDER COMPND MOL_ID: 1; COMPND 2 MOLECULE: WFAP1.1 STRUCTURE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTIFICIAL SEQUENCES; SOURCE 3 ORGANISM_TAXID: 81077; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGAND BINDING, FLUOROGENIC, FLUORESCENT PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.F.LIANG,J.Y.ZHU,P.L.LU REVDAT 1 27-NOV-24 8W6F 0 JRNL AUTH M.F.LIANG,J.Y.ZHU,P.L.LU JRNL TITL APO STRUCTURE OF HBC BINDER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 14734 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.340 REMARK 3 FREE R VALUE TEST SET COUNT : 787 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 25.4200 - 4.2700 0.99 2386 136 0.2260 0.2384 REMARK 3 2 4.2700 - 3.3900 0.98 2301 125 0.2424 0.2415 REMARK 3 3 3.3900 - 2.9700 1.00 2347 141 0.2654 0.3300 REMARK 3 4 2.9700 - 2.7000 1.00 2346 115 0.2798 0.3203 REMARK 3 5 2.6900 - 2.5000 1.00 2303 148 0.2587 0.3113 REMARK 3 6 2.5000 - 2.3500 0.97 2264 122 0.2503 0.3127 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) : 0.285 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.695 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.68 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 : 0.007 2668 REMARK 3 ANGLE : 1.090 3565 REMARK 3 CHIRALITY : 0.059 419 REMARK 3 PLANARITY : 0.008 455 REMARK 3 DIHEDRAL : 16.379 1087 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 8W6F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300040138. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 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 : CU FINE FOCUS 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 : CCD REMARK 200 DETECTOR MANUFACTURER : AGILENT ATLAS CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14804 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 25.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.310 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE, 20% W/V PEG1000, REMARK 280 0.1M SODIUM PHOSPHATE CITRATE PH4.2, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291.15K 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 46.20100 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 ASN A 37 REMARK 465 VAL A 38 REMARK 465 THR A 39 REMARK 465 THR A 123 REMARK 465 ASP A 124 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 ASN B 37 REMARK 465 VAL B 38 REMARK 465 THR B 39 REMARK 465 HIS B 164 REMARK 465 HIS B 165 REMARK 465 HIS B 166 REMARK 465 HIS B 167 REMARK 465 HIS B 168 REMARK 465 HIS B 169 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 GLU A 3 CG CD OE1 OE2 REMARK 470 ARG A 31 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 32 CG CD OE1 OE2 REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 GLU A 42 CG CD OE1 OE2 REMARK 470 GLU A 43 CG CD OE1 OE2 REMARK 470 ARG A 46 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 49 CG CD CE NZ REMARK 470 ARG A 87 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 LYS A 109 CG CD CE NZ REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 ARG A 116 CG CD NE CZ NH1 NH2 REMARK 470 THR A 122 OG1 CG2 REMARK 470 GLU A 125 CG CD OE1 OE2 REMARK 470 ARG A 129 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 130 CG CD OE1 OE2 REMARK 470 ARG A 136 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 137 CG CD OE1 OE2 REMARK 470 MET B 0 CG SD CE REMARK 470 GLU B 2 CG CD OE1 OE2 REMARK 470 GLU B 3 CG CD OE1 OE2 REMARK 470 ARG B 4 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 17 CG CD OE1 OE2 REMARK 470 GLU B 18 CG CD OE1 OE2 REMARK 470 ARG B 35 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 36 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 41 CG CD CE NZ REMARK 470 ARG B 45 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 46 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 56 CG CD CE NZ REMARK 470 GLU B 108 CG CD OE1 OE2 REMARK 470 LYS B 109 CG CD CE NZ REMARK 470 LYS B 111 CG CD CE NZ REMARK 470 LEU B 113 CG CD1 CD2 REMARK 470 LYS B 115 CG CD CE NZ REMARK 470 ARG B 129 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 158 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP B 1 -159.39 -93.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8W6E RELATED DB: PDB REMARK 900 8W6E IS THE COMPLEX FORM OF THIS PROTEIN. DBREF 8W6F A 0 169 PDB 8W6F 8W6F 0 169 DBREF 8W6F B 0 169 PDB 8W6F 8W6F 0 169 SEQRES 1 A 170 MET ASP GLU GLU ARG LEU LYS GLU ILE LEU GLU GLU LEU SEQRES 2 A 170 GLU ARG ILE ILE GLU GLU VAL LYS ARG LEU LEU GLU LYS SEQRES 3 A 170 ASP GLU ARG LEU LEU ARG GLU PHE TYR ARG ARG ASN VAL SEQRES 4 A 170 THR ASP LYS GLU GLU PHE ARG ARG VAL ILE LYS LEU ASP SEQRES 5 A 170 GLU GLU VAL MET LYS ARG SER GLU GLU LEU LEU LYS ARG SEQRES 6 A 170 ALA GLU GLU LEU LEU ARG GLU LEU GLU GLU LEU ILE ARG SEQRES 7 A 170 ARG ILE PRO PHE SER GLU GLU ILE ARG ARG GLU LEU GLU SEQRES 8 A 170 GLU ILE LEU ARG ARG LEU LYS GLU LEU TYR GLU GLU ALA SEQRES 9 A 170 LYS ARG LEU MET GLU LYS ALA LYS GLU LEU THR LYS ARG SEQRES 10 A 170 ILE LYS LYS ILE ASP THR THR ASP GLU LYS THR LEU ARG SEQRES 11 A 170 GLU TRP TYR GLU ILE VAL ARG GLU LEU LEU GLU ARG ALA SEQRES 12 A 170 LYS GLU ILE ILE GLU GLU ILE GLU ARG LEU LEU ARG ARG SEQRES 13 A 170 LEU LEU GLU ILE LEU GLY LEU GLU HIS HIS HIS HIS HIS SEQRES 14 A 170 HIS SEQRES 1 B 170 MET ASP GLU GLU ARG LEU LYS GLU ILE LEU GLU GLU LEU SEQRES 2 B 170 GLU ARG ILE ILE GLU GLU VAL LYS ARG LEU LEU GLU LYS SEQRES 3 B 170 ASP GLU ARG LEU LEU ARG GLU PHE TYR ARG ARG ASN VAL SEQRES 4 B 170 THR ASP LYS GLU GLU PHE ARG ARG VAL ILE LYS LEU ASP SEQRES 5 B 170 GLU GLU VAL MET LYS ARG SER GLU GLU LEU LEU LYS ARG SEQRES 6 B 170 ALA GLU GLU LEU LEU ARG GLU LEU GLU GLU LEU ILE ARG SEQRES 7 B 170 ARG ILE PRO PHE SER GLU GLU ILE ARG ARG GLU LEU GLU SEQRES 8 B 170 GLU ILE LEU ARG ARG LEU LYS GLU LEU TYR GLU GLU ALA SEQRES 9 B 170 LYS ARG LEU MET GLU LYS ALA LYS GLU LEU THR LYS ARG SEQRES 10 B 170 ILE LYS LYS ILE ASP THR THR ASP GLU LYS THR LEU ARG SEQRES 11 B 170 GLU TRP TYR GLU ILE VAL ARG GLU LEU LEU GLU ARG ALA SEQRES 12 B 170 LYS GLU ILE ILE GLU GLU ILE GLU ARG LEU LEU ARG ARG SEQRES 13 B 170 LEU LEU GLU ILE LEU GLY LEU GLU HIS HIS HIS HIS HIS SEQRES 14 B 170 HIS FORMUL 3 HOH *70(H2 O) HELIX 1 AA1 MET A 0 ARG A 36 1 37 HELIX 2 AA2 LYS A 41 ILE A 79 1 39 HELIX 3 AA3 SER A 82 LYS A 118 1 37 HELIX 4 AA4 LYS A 126 LEU A 160 1 35 HELIX 5 AA5 ASP B 1 ARG B 36 1 36 HELIX 6 AA6 LYS B 41 ILE B 79 1 39 HELIX 7 AA7 SER B 82 LYS B 118 1 37 HELIX 8 AA8 ASP B 124 LEU B 160 1 37 CRYST1 40.107 92.402 51.813 90.00 108.06 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 0.024933 0.000000 0.008131 0.00000 SCALE2 0.000000 0.010822 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020301 0.00000