HEADER DE NOVO PROTEIN 17-FEB-26 11CR TITLE CRYSTAL STRUCTURE OF ZN5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZN5; COMPND 3 CHAIN: A; COMPND 4 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 KEYWDS DE NOVO DESIGN, METALLOPROTEASES, ENZYME DESIGN, DEEP LEARNING KEYWDS 2 METHOD, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,A.CHEN,K.WU,A.KANG,H.NGUYEN,D.BAKER REVDAT 1 09-SEP-26 11CR 0 JRNL AUTH A.CHEN,K.WU,A.K.BERA,D.BAKER JRNL TITL COMPUTATIONAL DESIGN OF METALLOPROTEASES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 3.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 4541 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 453 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 64.4200 - 5.1500 1.00 1362 154 0.1995 0.2147 REMARK 3 2 5.1500 - 4.0900 1.00 1371 152 0.2488 0.2813 REMARK 3 3 4.0900 - 3.5700 1.00 1355 147 0.2991 0.3124 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) : 0.419 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.918 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 122.3 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 130.0 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 : 0.002 1697 REMARK 3 ANGLE : 0.395 2277 REMARK 3 CHIRALITY : 0.033 243 REMARK 3 PLANARITY : 0.004 302 REMARK 3 DIHEDRAL : 13.119 664 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): -11.6549 24.5254 -0.0437 REMARK 3 T TENSOR REMARK 3 T11: 1.1456 T22: 1.1885 REMARK 3 T33: 1.0544 T12: -0.1187 REMARK 3 T13: 0.0274 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 1.0928 L22: 2.4804 REMARK 3 L33: 0.7283 L12: -1.2172 REMARK 3 L13: -0.0471 L23: -0.6839 REMARK 3 S TENSOR REMARK 3 S11: -0.1515 S12: 0.0963 S13: 0.0193 REMARK 3 S21: -0.0980 S22: 0.2172 S23: -0.0327 REMARK 3 S31: 0.1279 S32: -0.0195 S33: -0.0329 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 11CR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1000305276. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97905 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4544 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.570 REMARK 200 RESOLUTION RANGE LOW (A) : 64.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.38100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 10.20 REMARK 200 R MERGE FOR SHELL (I) : 0.92400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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 (%): 69.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M GLYCINE PH 9.0 AND 55 % V/V PEG REMARK 280 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 53.66600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.98408 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.78367 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 53.66600 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 30.98408 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.78367 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 53.66600 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 30.98408 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 29.78367 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.96816 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 59.56733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 61.96816 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 59.56733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 61.96816 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 59.56733 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 TRP A 204 REMARK 465 SER A 205 REMARK 465 HIS A 206 REMARK 465 PRO A 207 REMARK 465 GLN A 208 REMARK 465 PHE A 209 REMARK 465 GLU A 210 REMARK 465 LYS A 211 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 SER A 202 59.37 -114.27 REMARK 500 REMARK 500 REMARK: NULL DBREF 11CR A -2 211 PDB 11CR 11CR -2 211 SEQRES 1 A 214 MET SER GLY MET THR ALA GLU GLU LEU ALA GLU ARG ILE SEQRES 2 A 214 GLY GLU ALA LEU ALA ARG GLY ARG TRP ASP GLU VAL TYR SEQRES 3 A 214 ALA LEU GLY ALA TYR ALA PHE LEU THR LEU THR PRO GLU SEQRES 4 A 214 GLU ILE GLU GLU MET ARG ARG ARG LEU ARG GLU VAL LEU SEQRES 5 A 214 ARG GLU GLU LEU LYS LYS LEU GLY LYS THR TYR SER ASP SEQRES 6 A 214 GLU GLU VAL ASP ARG LEU VAL GLU ALA ALA VAL TYR GLU SEQRES 7 A 214 GLY GLU ALA SER ALA VAL VAL VAL ARG ARG TYR ARG GLU SEQRES 8 A 214 GLU GLY LEU PRO GLU ASP MET THR ASP GLU GLN LEU PHE SEQRES 9 A 214 GLU LEU GLY MET LEU HIS GLU ALA TYR HIS VAL ASN PHE SEQRES 10 A 214 GLY ASP ALA TYR VAL VAL ALA ASP GLY LYS GLU GLY ILE SEQRES 11 A 214 VAL GLU VAL LEU VAL ALA ARG THR GLU GLU GLU LEU GLU SEQRES 12 A 214 GLU ALA ARG ARG LEU ALA GLU ARG ALA ARG GLU GLU GLY SEQRES 13 A 214 LYS GLU VAL ARG PHE PHE LYS LYS GLY GLU GLU GLU ALA SEQRES 14 A 214 VAL ILE GLU TRP LEU ARG GLU VAL ALA GLU LYS TYR PRO SEQRES 15 A 214 LYS VAL ARG GLU GLY LEU ILE GLU GLY THR ARG ARG LEU SEQRES 16 A 214 LEU GLU GLU TYR ARG LYS ILE VAL GLY SER ALA TRP SER SEQRES 17 A 214 HIS PRO GLN PHE GLU LYS HELIX 1 AA1 THR A 2 GLY A 17 1 16 HELIX 2 AA2 ARG A 18 LEU A 33 1 16 HELIX 3 AA3 THR A 34 LEU A 56 1 23 HELIX 4 AA4 SER A 61 GLY A 90 1 30 HELIX 5 AA5 THR A 96 HIS A 111 1 16 HELIX 6 AA6 VAL A 112 GLY A 115 5 4 HELIX 7 AA7 THR A 135 GLY A 153 1 19 HELIX 8 AA8 GLU A 163 TYR A 178 1 16 HELIX 9 AA9 TYR A 178 GLY A 201 1 24 SHEET 1 AA1 3 ILE A 127 VAL A 132 0 SHEET 2 AA1 3 ALA A 117 ASP A 122 -1 N VAL A 120 O GLU A 129 SHEET 3 AA1 3 VAL A 156 PHE A 159 -1 O PHE A 159 N ALA A 117 CRYST1 107.332 107.332 89.351 90.00 90.00 120.00 H 3 9 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 0.009317 0.005379 0.000000 0.00000 SCALE2 0.000000 0.010758 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011192 0.00000 MASTER 257 0 0 9 3 0 0 6 1675 1 0 17 END