HEADER STRUCTURAL PROTEIN 17-JAN-25 9LLO TITLE A DESIGNED HETEROTRIMER COMBINING NATURAL AND SYNTHETIC FRAGMENTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN-LIKE PEPTIDE CHAIN A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: COLLAGEN-LIKE PEPTIDE CHAIN B; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: COLLAGEN-LIKE PEPTIDE CHAIN C; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: CHEMICAL PRODUCTION METAGENOME; SOURCE 4 ORGANISM_TAXID: 2495586; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: CHEMICAL PRODUCTION METAGENOME; SOURCE 8 ORGANISM_TAXID: 2495586; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: CHEMICAL PRODUCTION METAGENOME; SOURCE 12 ORGANISM_TAXID: 2495586 KEYWDS HETEROTRIMER, COLLAGEN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.X.ZHANG,F.XU,S.L.FAN REVDAT 1 22-JUL-26 9LLO 0 JRNL AUTH R.X.ZHANG,C.G.QIU,R.ZSCHAU,M.ZACHARIAS,S.L.FAN,V.NANDA,F.XU JRNL TITL DESIGN OF HETEROSPECIFIC COLLAGENS DIRECTED BY CHEMICALLY JRNL TITL 2 DIVERSE SURFACE INTERACTIONS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21RC1_5109: ???) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 9946 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 509 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 2.8500 - 2.2600 1.00 2351 138 0.1830 0.2351 REMARK 3 2 2.2600 - 1.9800 1.00 2337 102 0.1661 0.2232 REMARK 3 3 1.9800 - 1.8000 0.97 2238 134 0.2090 0.2856 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.340 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : 0.046 83 REMARK 3 PLANARITY : 0.008 162 REMARK 3 DIHEDRAL : 14.155 319 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 9LLO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 21-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1300055894. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-24 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 : BL02U1 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 EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9946 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 29.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 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 (%): 44.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CITRATE TRIBASIC PH 7.0 REMARK 280 20% W/V POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 7.58050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.52300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.34050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.52300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 7.58050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.34050 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: 7340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 B 34 CG CD CE NZ 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 C 104 O HOH C 134 2.10 REMARK 500 O HOH B 148 O HOH B 150 2.15 REMARK 500 REMARK 500 REMARK: NULL DBREF 9LLO A 1 38 PDB 9LLO 9LLO 1 38 DBREF 9LLO B 1 38 PDB 9LLO 9LLO 1 38 DBREF 9LLO C 1 38 PDB 9LLO 9LLO 1 38 SEQRES 1 A 38 TYR GLY ASP LYS GLY ASP ASP GLY ASP ARG GLY ASP ASN SEQRES 2 A 38 GLY ILE HYP GLY PRO LYS GLY GLU LYS GLY GLU HYP GLY SEQRES 3 A 38 ASP ARG GLY ASP ASN GLY ASP MET GLY ASP ASN GLY SEQRES 1 B 38 TYR GLY PRO LYS GLY PRO LYS GLY PRO LYS GLY PRO LYS SEQRES 2 B 38 GLY ILE HYP GLY PRO LYS GLY GLU LYS GLY GLU HYP GLY SEQRES 3 B 38 PRO LYS GLY PRO LYS GLY PRO LYS GLY PRO LYS GLY SEQRES 1 C 38 TYR GLY PRO PRO GLY ASN PRO GLY PRO PRO GLY PHE PRO SEQRES 2 C 38 GLY LEU HYP GLY PRO LYS GLY ASP ARG GLY ASP ALA GLY SEQRES 3 C 38 PRO PRO GLY PHE PRO GLY PRO PRO GLY TYR PRO GLY HET HYP A 16 8 HET HYP A 25 8 HET HYP B 16 8 HET HYP B 25 8 HET HYP C 16 8 HETNAM HYP 4-HYDROXYPROLINE HETSYN HYP HYDROXYPROLINE FORMUL 1 HYP 5(C5 H9 N O3) FORMUL 4 HOH *225(H2 O) LINK C ILE A 15 N HYP A 16 1555 1555 1.33 LINK C HYP A 16 N GLY A 17 1555 1555 1.33 LINK C GLU A 24 N HYP A 25 1555 1555 1.33 LINK C HYP A 25 N GLY A 26 1555 1555 1.33 LINK C ILE B 15 N HYP B 16 1555 1555 1.33 LINK C HYP B 16 N GLY B 17 1555 1555 1.33 LINK C GLU B 24 N HYP B 25 1555 1555 1.33 LINK C HYP B 25 N GLY B 26 1555 1555 1.33 LINK C LEU C 15 N HYP C 16 1555 1555 1.33 LINK C HYP C 16 N GLY C 17 1555 1555 1.33 CRYST1 15.161 54.681 119.046 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 0.065959 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018288 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008400 0.00000 CONECT 103 109 CONECT 109 103 110 115 CONECT 110 109 111 113 CONECT 111 110 112 117 CONECT 112 111 CONECT 113 110 114 CONECT 114 113 115 116 CONECT 115 109 114 CONECT 116 114 CONECT 117 111 CONECT 165 172 CONECT 172 165 173 178 CONECT 173 172 174 176 CONECT 174 173 175 180 CONECT 175 174 CONECT 176 173 177 CONECT 177 176 178 179 CONECT 178 172 177 CONECT 179 177 CONECT 180 174 CONECT 366 372 CONECT 372 366 373 378 CONECT 373 372 374 376 CONECT 374 373 375 380 CONECT 375 374 CONECT 376 373 377 CONECT 377 376 378 379 CONECT 378 372 377 CONECT 379 377 CONECT 380 374 CONECT 428 435 CONECT 435 428 436 441 CONECT 436 435 437 439 CONECT 437 436 438 443 CONECT 438 437 CONECT 439 436 440 CONECT 440 439 441 442 CONECT 441 435 440 CONECT 442 440 CONECT 443 437 CONECT 619 625 CONECT 625 619 626 631 CONECT 626 625 627 629 CONECT 627 626 628 633 CONECT 628 627 CONECT 629 626 630 CONECT 630 629 631 632 CONECT 631 625 630 CONECT 632 630 CONECT 633 627 MASTER 213 0 5 0 0 0 0 6 1000 3 50 9 END