HEADER DE NOVO PROTEIN 18-JAN-25 9LM8 TITLE CRYSTAL STRUCTURE OF BVFP-PFR21 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BVFP-PFR21; 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; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NEAR-INFRARED PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.DING,Z.XU,L.CAO REVDAT 1 28-JAN-26 9LM8 0 JRNL AUTH G.DING,Z.XU,L.CAO JRNL TITL DE NOVO DESIGN OF NIR-I/II FLUORESCENT PROTEINS FOR IN VIVO JRNL TITL 2 DEEP TISSUE IMAGING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.45 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 12954 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1299 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 42.8000 - 5.0900 0.91 1325 145 0.2323 0.2631 REMARK 3 2 5.0900 - 4.0400 0.90 1340 149 0.2154 0.2746 REMARK 3 3 4.0400 - 3.5300 0.89 1305 146 0.2217 0.2746 REMARK 3 4 3.5300 - 3.2100 0.90 1322 147 0.2470 0.2988 REMARK 3 5 3.2100 - 2.9800 0.91 1337 141 0.2507 0.3095 REMARK 3 6 2.9800 - 2.8000 0.89 1313 147 0.2664 0.3157 REMARK 3 7 2.8000 - 2.6600 0.86 1265 141 0.2536 0.2750 REMARK 3 8 2.6600 - 2.5500 0.84 1228 138 0.2510 0.3298 REMARK 3 9 2.5500 - 2.4500 0.84 1220 145 0.2592 0.3092 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.000 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 : 0.003 NULL REMARK 3 ANGLE : 0.560 NULL REMARK 3 CHIRALITY : 0.033 476 REMARK 3 PLANARITY : 0.005 537 REMARK 3 DIHEDRAL : 4.664 437 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): 4.6152 -24.6320 18.8108 REMARK 3 T TENSOR REMARK 3 T11: 0.1475 T22: 0.2273 REMARK 3 T33: 0.2481 T12: 0.0045 REMARK 3 T13: -0.1160 T23: -0.0195 REMARK 3 L TENSOR REMARK 3 L11: 1.5689 L22: 1.7011 REMARK 3 L33: 1.0623 L12: -0.7524 REMARK 3 L13: -0.6485 L23: 0.3144 REMARK 3 S TENSOR REMARK 3 S11: -0.1155 S12: 0.1663 S13: -0.1765 REMARK 3 S21: -0.2036 S22: -0.0396 S23: 0.2295 REMARK 3 S31: 0.2050 S32: 0.0284 S33: 0.0803 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 9LM8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 02-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1300055944. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 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) : 0.987 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14135 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 42.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V/V 2-PROPANOL; 0.1 M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE (PH 5.0); AND 26% V/V POLYETHYLENE REMARK 280 GLYCOL 400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 410 O HOH A 420 1.85 REMARK 500 OD2 ASP A 370 O HOH A 401 1.93 REMARK 500 OD1 ASP A 1 O HOH A 402 2.08 REMARK 500 O HOH A 430 O HOH A 437 2.15 REMARK 500 OD2 ASP A 49 O HOH A 403 2.17 REMARK 500 OXT LYS A 381 O HOH A 404 2.17 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 OD2 ASP A 1 N ALA A 149 1644 2.08 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 20 41.60 -79.15 REMARK 500 REMARK 500 REMARK: NULL DBREF 9LM8 A 1 381 PDB 9LM8 9LM8 1 381 SEQRES 1 A 381 ASP ALA PHE ALA LYS THR GLN ALA ALA ILE GLN LYS LEU SEQRES 2 A 381 VAL GLU LYS HIS LEU ALA LYS VAL PRO GLN GLY GLY PRO SEQRES 3 A 381 TYR ASP GLU TYR SER ALA TYR GLN CYS GLU ARG ASP ARG SEQRES 4 A 381 ARG LEU ALA GLU LEU HIS ALA ALA GLY ASP GLU ALA ALA SEQRES 5 A 381 TYR LEU ALA LEU VAL GLU GLU SER PHE GLU TYR THR LYS SEQRES 6 A 381 LYS PHE PHE LEU SER ASN LYS ASP VAL GLU SER VAL GLU SEQRES 7 A 381 ILE SER ILE GLU PHE VAL GLU GLU ILE ILE LYS VAL ALA SEQRES 8 A 381 ARG GLU LEU GLY ASP ARG LEU THR ALA GLU SER ALA GLU SEQRES 9 A 381 ARG LYS LEU GLU LEU LEU LYS GLU ILE LEU LYS GLU ILE SEQRES 10 A 381 LYS GLU SER ALA ILE ARG VAL ALA LYS LEU ALA THR GLU SEQRES 11 A 381 VAL ARG ARG PHE ALA GLU GLU LEU ALA GLU GLU VAL LEU SEQRES 12 A 381 ARG VAL GLY GLY GLU ALA MET ARG PRO TYR ALA GLU MET SEQRES 13 A 381 VAL ARG HIS LEU GLY GLU ALA ALA VAL ALA ALA LEU THR SEQRES 14 A 381 GLY ARG ALA GLU GLU ALA ASP ARG LEU VAL ARG ASP VAL SEQRES 15 A 381 LEU GLU MET ALA ARG GLU VAL GLY ALA GLU GLY LEU ALA SEQRES 16 A 381 ARG LEU LEU GLU ARG VAL HIS ARG GLU ALA ARG GLU LEU SEQRES 17 A 381 LEU ARG GLU GLY ARG ARG GLU GLU ALA ALA ALA LEU VAL SEQRES 18 A 381 LEU ALA ALA ALA LEU ALA ALA GLY ALA VAL ALA VAL ALA SEQRES 19 A 381 GLU ALA TYR VAL ARG LEU GLY GLN PRO ILE ARG LEU ILE SEQRES 20 A 381 ALA GLU TYR VAL ALA GLU ARG LEU VAL GLU LEU ALA GLU SEQRES 21 A 381 LEU LEU ARG ARG LEU GLY VAL PRO LEU ARG ARG ILE ILE SEQRES 22 A 381 ARG LEU LEU GLU GLU VAL LEU ARG VAL VAL ALA GLU ALA SEQRES 23 A 381 LEU ARG ARG ALA GLY VAL PRO GLU PRO GLU ILE ARG LYS SEQRES 24 A 381 VAL GLU ALA ALA ALA TYR ILE ARG LEU ALA ALA TYR LEU SEQRES 25 A 381 LEU ARG GLN LEU GLY TYR GLU ALA LEU ALA LYS ARG LEU SEQRES 26 A 381 LEU GLU ALA ARG GLU LEU LEU LEU GLU GLY ARG VAL GLU SEQRES 27 A 381 GLU ALA ALA LYS LEU LEU GLU GLU VAL TYR ALA LEU PHE SEQRES 28 A 381 GLN ARG GLU ILE GLU ARG LEU GLY PHE GLU ALA PRO GLU SEQRES 29 A 381 GLU LEU ARG VAL ALA ASP LEU LEU LEU ALA ARG ALA ILE SEQRES 30 A 381 ALA LEU ILE LYS FORMUL 2 HOH *37(H2 O) HELIX 1 AA1 PHE A 3 LYS A 12 1 10 HELIX 2 AA2 GLU A 15 LYS A 20 1 6 HELIX 3 AA3 GLY A 25 ALA A 47 1 23 HELIX 4 AA4 ASP A 49 LYS A 72 1 24 HELIX 5 AA5 ASP A 73 GLY A 95 1 23 HELIX 6 AA6 ASP A 96 GLY A 147 1 52 HELIX 7 AA7 MET A 150 GLY A 170 1 21 HELIX 8 AA8 ARG A 171 GLY A 190 1 20 HELIX 9 AA9 ALA A 191 GLU A 211 1 21 HELIX 10 AB1 ARG A 213 LEU A 240 1 28 HELIX 11 AB2 PRO A 243 GLY A 266 1 24 HELIX 12 AB3 PRO A 268 GLY A 291 1 24 HELIX 13 AB4 PRO A 293 GLN A 315 1 23 HELIX 14 AB5 TYR A 318 GLU A 334 1 17 HELIX 15 AB6 ARG A 336 GLY A 359 1 24 HELIX 16 AB7 PHE A 360 ALA A 362 5 3 HELIX 17 AB8 PRO A 363 LYS A 381 1 19 CRYST1 41.625 45.576 59.021 102.75 102.06 102.21 P 1 1 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 0.024024 0.005199 0.006841 0.00000 SCALE2 0.000000 0.022449 0.006475 0.00000 SCALE3 0.000000 0.000000 0.018032 0.00000 MASTER 251 0 0 17 0 0 0 6 3054 1 0 30 END