HEADER DE NOVO PROTEIN 22-JUN-25 9VKD TITLE DE NOVO DESIGNED ZINC HYDROLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED ZINC HYDROLASE 2-8; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.1; 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 BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DE NOVO DESIGNED ZINC HYDROLASE, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.YITAO,C.LONGXING REVDAT 1 24-JUN-26 9VKD 0 JRNL AUTH K.YITAO,C.LONGXING JRNL TITL INTEGRATING MACHINE-LEARNING AND ULTRA-HIGH-THROUGHPUT JRNL TITL 2 SCREENING FOR ENZYME SPACES EXPLORATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.150 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 5871 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.303 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 584 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 29.9300 - 3.6500 0.99 1426 165 0.2374 0.2958 REMARK 3 2 3.6500 - 2.9000 0.96 1317 146 0.2718 0.3122 REMARK 3 3 2.9000 - 2.5300 0.93 1282 140 0.2424 0.3110 REMARK 3 4 2.5300 - 2.3000 0.93 1262 133 0.2401 0.2984 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.33 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 : 0.002 996 REMARK 3 ANGLE : 0.356 1320 REMARK 3 CHIRALITY : 0.030 145 REMARK 3 PLANARITY : 0.002 169 REMARK 3 DIHEDRAL : 3.321 126 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 9VKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 24-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1300059181. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-24 REMARK 200 TEMPERATURE (KELVIN) : 181 REMARK 200 PH : NULL 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) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6153 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 29.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.19260 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34670 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 12.78 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 (%): 46.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 3000, 100 MM IMIDAZOLE/ REMARK 280 HYDROCHLORIC ACID PH 8.0, 200 MM ZINC ACETATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 52.01400 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 26.00700 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.00700 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.01400 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 ZN ZN A 205 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 319 LIES ON A SPECIAL POSITION. 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 GLU A 44 62.03 -117.96 REMARK 500 ASN A 63 55.65 -112.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 206 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 5 OE1 REMARK 620 2 GLU A 20 OE2 52.2 REMARK 620 3 GLU A 90 OE1 125.6 78.9 REMARK 620 4 GLU A 90 OE2 99.4 91.5 55.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 6 OE1 REMARK 620 2 GLU A 46 OE2 90.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 207 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 15 ND1 REMARK 620 2 HIS A 19 NE2 110.6 REMARK 620 3 HOH A 321 O 174.4 73.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 26 OE2 REMARK 620 2 GLU A 29 OE2 131.7 REMARK 620 3 GLU A 78 OE2 80.2 70.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 205 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 44 OE2 REMARK 620 2 GLU A 44 OE2 0.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 321 O REMARK 620 2 HOH A 354 O 137.0 REMARK 620 N 1 DBREF 9VKD A 1 122 PDB 9VKD 9VKD 1 122 SEQRES 1 A 122 GLY PRO MET GLU GLU GLU ILE ALA LYS LYS ALA LEU GLU SEQRES 2 A 122 LEU HIS LYS GLU ALA HIS GLU SER SER LYS ASN ASP GLU SEQRES 3 A 122 GLU ILE GLU LYS LYS MET LYS GLU LYS ALA GLU GLU TYR SEQRES 4 A 122 LYS LYS LYS GLY GLU PRO GLU LEU ALA GLU MET ILE GLU SEQRES 5 A 122 LYS ILE THR GLU ASN ALA ILE LYS LEU HIS ASN ALA LYS SEQRES 6 A 122 THR GLU GLU GLU LYS ALA VAL ARG LYS ALA VAL GLN GLU SEQRES 7 A 122 GLY PHE GLU LEU TYR GLU LYS ALA LYS ASP GLU GLU ALA SEQRES 8 A 122 LYS LEU LYS ILE ALA ARG LEU ILE VAL GLU ILE ILE THR SEQRES 9 A 122 THR TYR ASP ALA LYS LYS ALA GLU GLU LEU LEU LYS GLU SEQRES 10 A 122 ALA LYS LYS ILE ALA HET ACT A 201 4 HET NA A 202 1 HET ZN A 203 1 HET ZN A 204 1 HET ZN A 205 1 HET ZN A 206 1 HET ZN A 207 1 HETNAM ACT ACETATE ION HETNAM NA SODIUM ION HETNAM ZN ZINC ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 NA NA 1+ FORMUL 4 ZN 5(ZN 2+) FORMUL 9 HOH *80(H2 O) HELIX 1 AA1 GLY A 1 SER A 22 1 22 HELIX 2 AA2 ASN A 24 LYS A 42 1 19 HELIX 3 AA3 GLU A 44 ASN A 63 1 20 HELIX 4 AA4 THR A 66 LYS A 85 1 20 HELIX 5 AA5 ASP A 88 TYR A 106 1 19 HELIX 6 AA6 ASP A 107 LYS A 120 1 14 LINK OE1 GLU A 5 ZN ZN A 206 1555 3655 2.09 LINK OE1 GLU A 6 ZN ZN A 204 1555 6555 2.31 LINK ND1 HIS A 15 ZN ZN A 207 1555 1555 2.40 LINK NE2 HIS A 19 ZN ZN A 207 1555 1555 2.15 LINK OE2 GLU A 20 ZN ZN A 206 1555 1555 2.09 LINK OE2 GLU A 26 ZN ZN A 203 1555 4545 2.29 LINK OE2 GLU A 29 ZN ZN A 203 1555 4545 2.34 LINK OE2 GLU A 44 ZN ZN A 205 1555 1555 2.12 LINK OE2 GLU A 44 ZN ZN A 205 1555 6555 2.12 LINK OE2 GLU A 46 ZN ZN A 204 1555 1555 2.05 LINK OE2 GLU A 78 ZN ZN A 203 1555 1555 2.16 LINK OE1 GLU A 90 ZN ZN A 206 1555 3655 2.55 LINK OE2 GLU A 90 ZN ZN A 206 1555 3655 2.13 LINK NA NA A 202 O HOH A 321 1555 1555 3.06 LINK NA NA A 202 O HOH A 354 1555 1555 2.28 LINK ZN ZN A 207 O HOH A 321 1555 1555 2.32 CRYST1 53.874 53.874 78.021 90.00 90.00 120.00 P 32 2 1 6 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 0.018562 0.010717 0.000000 0.00000 SCALE2 0.000000 0.021433 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012817 0.00000 CONECT 114 996 CONECT 150 996 CONECT 159 995 CONECT 359 994 CONECT 375 993 CONECT 630 992 CONECT 987 988 989 990 CONECT 988 987 CONECT 989 987 CONECT 990 987 CONECT 991 1017 1050 CONECT 992 630 CONECT 993 375 CONECT 994 359 CONECT 995 159 CONECT 996 114 150 1017 CONECT 1017 991 996 CONECT 1050 991 MASTER 277 0 7 6 0 0 0 6 1075 1 18 10 END