HEADER HYDROLASE 13-MAR-18 5ZHW TITLE VANYB IN COMPLEX WITH D-ALANINE-D-ALANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DD-PEPTIDASE; COMPND 5 EC: 3.4.16.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS V583; SOURCE 3 ORGANISM_TAXID: 226185; SOURCE 4 STRAIN: ATCC 700802 / V583; SOURCE 5 GENE: VANYB, EF_2297; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VANCOMYCIN RESISTANCE, PEPTIDASE, METALLOPEPTIDASE FAMILY M15, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.S.KIM,H.HAHN REVDAT 2 22-NOV-23 5ZHW 1 LINK REVDAT 1 05-SEP-18 5ZHW 0 JRNL AUTH H.S.KIM,H.HAHN,J.KIM,D.M.JANG,J.Y.LEE,J.M.BACK,H.N.IM,H.KIM, JRNL AUTH 2 B.W.HAN,S.W.SUH JRNL TITL STRUCTURAL BASIS FOR THE SUBSTRATE RECOGNITION OF JRNL TITL 2 PEPTIDOGLYCAN PENTAPEPTIDES BY ENTEROCOCCUS FAECALIS VANYB. JRNL REF INT. J. BIOL. MACROMOL. V. 119 335 2018 JRNL REFN ISSN 1879-0003 JRNL PMID 30016658 JRNL DOI 10.1016/J.IJBIOMAC.2018.07.081 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 18878 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 988 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1357 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.2010 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.2550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2924 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.41000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.51000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.31000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.243 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.187 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.941 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3042 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2714 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4124 ; 1.339 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6302 ; 0.946 ; 3.006 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 360 ; 5.712 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;34.024 ;24.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 482 ;12.719 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.504 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 436 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3400 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 624 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1452 ; 2.273 ; 3.548 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1452 ; 2.270 ; 3.548 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1808 ; 3.546 ; 5.293 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1809 ; 3.546 ; 5.296 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1589 ; 3.153 ; 4.032 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1590 ; 3.152 ; 4.034 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2316 ; 4.953 ; 5.882 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3463 ; 6.536 ;41.545 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3464 ; 6.535 ;41.563 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5ZHW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300007110. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-12 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19873 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 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: NULL REMARK 200 STARTING MODEL: 5ZHF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1500, GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 42.93050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.28900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.93050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.28900 REMARK 290 SMTRY3 4 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 MSE A 49 REMARK 465 ALA A 50 REMARK 465 SER A 51 REMARK 465 THR A 52 REMARK 465 GLN A 53 REMARK 465 LEU A 54 REMARK 465 PRO A 55 REMARK 465 PRO A 56 REMARK 465 ILE A 57 REMARK 465 PRO A 58 REMARK 465 ALA A 59 REMARK 465 THR A 60 REMARK 465 HIS A 61 REMARK 465 THR A 62 REMARK 465 GLY A 63 REMARK 465 SER A 64 REMARK 465 GLY A 65 REMARK 465 THR A 66 REMARK 465 GLY A 67 REMARK 465 VAL A 68 REMARK 465 ALA A 69 REMARK 465 GLU A 70 REMARK 465 ASN A 71 REMARK 465 PRO A 72 REMARK 465 GLU A 73 REMARK 465 GLU A 74 REMARK 465 ASN A 75 REMARK 465 THR A 76 REMARK 465 LEU A 77 REMARK 465 ALA A 78 REMARK 465 THR A 79 REMARK 465 ALA A 80 REMARK 465 LYS A 81 REMARK 465 GLU A 82 REMARK 465 GLN A 83 REMARK 465 GLY A 84 REMARK 465 ASP A 85 REMARK 465 GLU A 86 REMARK 465 GLN A 87 REMARK 465 LEU A 269 REMARK 465 GLU A 270 REMARK 465 HIS A 271 REMARK 465 HIS A 272 REMARK 465 HIS A 273 REMARK 465 HIS A 274 REMARK 465 HIS A 275 REMARK 465 HIS A 276 REMARK 465 MSE B 49 REMARK 465 ALA B 50 REMARK 465 SER B 51 REMARK 465 THR B 52 REMARK 465 GLN B 53 REMARK 465 LEU B 54 REMARK 465 PRO B 55 REMARK 465 PRO B 56 REMARK 465 ILE B 57 REMARK 465 PRO B 58 REMARK 465 ALA B 59 REMARK 465 THR B 60 REMARK 465 HIS B 61 REMARK 465 THR B 62 REMARK 465 GLY B 63 REMARK 465 SER B 64 REMARK 465 GLY B 65 REMARK 465 THR B 66 REMARK 465 GLY B 67 REMARK 465 VAL B 68 REMARK 465 ALA B 69 REMARK 465 GLU B 70 REMARK 465 ASN B 71 REMARK 465 PRO B 72 REMARK 465 GLU B 73 REMARK 465 GLU B 74 REMARK 465 ASN B 75 REMARK 465 THR B 76 REMARK 465 LEU B 77 REMARK 465 ALA B 78 REMARK 465 THR B 79 REMARK 465 ALA B 80 REMARK 465 LYS B 81 REMARK 465 GLU B 82 REMARK 465 GLN B 83 REMARK 465 GLY B 84 REMARK 465 ASP B 85 REMARK 465 GLU B 86 REMARK 465 GLN B 87 REMARK 465 LEU B 269 REMARK 465 GLU B 270 REMARK 465 HIS B 271 REMARK 465 HIS B 272 REMARK 465 HIS B 273 REMARK 465 HIS B 274 REMARK 465 HIS B 275 REMARK 465 HIS B 276 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 GLN A 103 54.43 -115.98 REMARK 500 ASN B 95 -174.13 -170.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PG4 A 305 REMARK 610 PG4 B 305 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 CU A 301 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 188 NE2 REMARK 620 2 ASP A 195 OD1 102.1 REMARK 620 3 HIS A 241 ND1 101.3 108.5 REMARK 620 4 DAL A 303 O 129.7 108.1 105.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 301 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 188 NE2 REMARK 620 2 ASP B 195 OD1 101.0 REMARK 620 3 HIS B 241 ND1 106.1 106.0 REMARK 620 4 DAL B 303 O 129.5 99.4 111.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DAL A 302 and DAL A REMARK 800 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DAL B 302 and DAL B REMARK 800 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ZHF RELATED DB: PDB REMARK 900 THE SMAE PROTEIN WITHOUT BOUND DIPEPTIDE DBREF 5ZHW A 52 268 UNP Q47746 VANY_ENTFA 52 268 DBREF 5ZHW B 52 268 UNP Q47746 VANY_ENTFA 52 268 SEQADV 5ZHW MSE A 49 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW ALA A 50 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW SER A 51 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW LEU A 269 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW GLU A 270 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW HIS A 271 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW HIS A 272 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW HIS A 273 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW HIS A 274 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW HIS A 275 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW HIS A 276 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW MSE B 49 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW ALA B 50 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW SER B 51 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW LEU B 269 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW GLU B 270 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW HIS B 271 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW HIS B 272 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW HIS B 273 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW HIS B 274 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW HIS B 275 UNP Q47746 EXPRESSION TAG SEQADV 5ZHW HIS B 276 UNP Q47746 EXPRESSION TAG SEQRES 1 A 228 MSE ALA SER THR GLN LEU PRO PRO ILE PRO ALA THR HIS SEQRES 2 A 228 THR GLY SER GLY THR GLY VAL ALA GLU ASN PRO GLU GLU SEQRES 3 A 228 ASN THR LEU ALA THR ALA LYS GLU GLN GLY ASP GLU GLN SEQRES 4 A 228 GLU TRP SER LEU ILE LEU VAL ASN ARG GLN ASN PRO ILE SEQRES 5 A 228 PRO ALA GLN TYR ASP VAL GLU LEU GLU GLN LEU SER ASN SEQRES 6 A 228 GLY GLU ARG ILE ASP ILE ARG ILE SER PRO TYR LEU GLN SEQRES 7 A 228 ASP LEU PHE ASP ALA ALA ARG ALA ASP GLY VAL TYR PRO SEQRES 8 A 228 ILE VAL ALA SER GLY TYR ARG THR THR GLU LYS GLN GLN SEQRES 9 A 228 GLU ILE MSE ASP GLU LYS VAL ALA GLU TYR LYS ALA LYS SEQRES 10 A 228 GLY TYR THR SER ALA GLN ALA LYS ALA GLU ALA GLU THR SEQRES 11 A 228 TRP VAL ALA VAL PRO GLY THR SER GLU HIS GLN LEU GLY SEQRES 12 A 228 LEU ALA VAL ASP ILE ASN ALA ASP GLY ILE HIS SER THR SEQRES 13 A 228 GLY ASN GLU VAL TYR ARG TRP LEU ASP GLU ASN SER TYR SEQRES 14 A 228 ARG PHE GLY PHE ILE ARG ARG TYR PRO PRO ASP LYS THR SEQRES 15 A 228 GLU ILE THR GLY VAL SER ASN GLU PRO TRP HIS TYR ARG SEQRES 16 A 228 TYR VAL GLY ILE GLU ALA ALA THR LYS ILE TYR HIS GLN SEQRES 17 A 228 GLY LEU CYS LEU GLU GLU TYR LEU ASN THR GLU LYS LEU SEQRES 18 A 228 GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 228 MSE ALA SER THR GLN LEU PRO PRO ILE PRO ALA THR HIS SEQRES 2 B 228 THR GLY SER GLY THR GLY VAL ALA GLU ASN PRO GLU GLU SEQRES 3 B 228 ASN THR LEU ALA THR ALA LYS GLU GLN GLY ASP GLU GLN SEQRES 4 B 228 GLU TRP SER LEU ILE LEU VAL ASN ARG GLN ASN PRO ILE SEQRES 5 B 228 PRO ALA GLN TYR ASP VAL GLU LEU GLU GLN LEU SER ASN SEQRES 6 B 228 GLY GLU ARG ILE ASP ILE ARG ILE SER PRO TYR LEU GLN SEQRES 7 B 228 ASP LEU PHE ASP ALA ALA ARG ALA ASP GLY VAL TYR PRO SEQRES 8 B 228 ILE VAL ALA SER GLY TYR ARG THR THR GLU LYS GLN GLN SEQRES 9 B 228 GLU ILE MSE ASP GLU LYS VAL ALA GLU TYR LYS ALA LYS SEQRES 10 B 228 GLY TYR THR SER ALA GLN ALA LYS ALA GLU ALA GLU THR SEQRES 11 B 228 TRP VAL ALA VAL PRO GLY THR SER GLU HIS GLN LEU GLY SEQRES 12 B 228 LEU ALA VAL ASP ILE ASN ALA ASP GLY ILE HIS SER THR SEQRES 13 B 228 GLY ASN GLU VAL TYR ARG TRP LEU ASP GLU ASN SER TYR SEQRES 14 B 228 ARG PHE GLY PHE ILE ARG ARG TYR PRO PRO ASP LYS THR SEQRES 15 B 228 GLU ILE THR GLY VAL SER ASN GLU PRO TRP HIS TYR ARG SEQRES 16 B 228 TYR VAL GLY ILE GLU ALA ALA THR LYS ILE TYR HIS GLN SEQRES 17 B 228 GLY LEU CYS LEU GLU GLU TYR LEU ASN THR GLU LYS LEU SEQRES 18 B 228 GLU HIS HIS HIS HIS HIS HIS MODRES 5ZHW MSE A 155 MET MODIFIED RESIDUE MODRES 5ZHW MSE B 155 MET MODIFIED RESIDUE HET MSE A 155 8 HET MSE B 155 8 HET CU A 301 1 HET DAL A 302 6 HET DAL A 303 5 HET GOL A 304 6 HET PG4 A 305 10 HET CU B 301 1 HET DAL B 302 6 HET DAL B 303 5 HET GOL B 304 6 HET PG4 B 305 10 HETNAM MSE SELENOMETHIONINE HETNAM CU COPPER (II) ION HETNAM DAL D-ALANINE HETNAM GOL GLYCEROL HETNAM PG4 TETRAETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 CU 2(CU 2+) FORMUL 4 DAL 4(C3 H7 N O2) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 7 PG4 2(C8 H18 O5) FORMUL 13 HOH *108(H2 O) HELIX 1 AA1 GLU A 88 ILE A 92 5 5 HELIX 2 AA2 ILE A 121 ASP A 135 1 15 HELIX 3 AA3 THR A 147 LYS A 165 1 19 HELIX 4 AA4 THR A 168 THR A 178 1 11 HELIX 5 AA5 SER A 186 GLY A 191 5 6 HELIX 6 AA6 THR A 204 SER A 216 1 13 HELIX 7 AA7 TYR A 217 PHE A 219 5 3 HELIX 8 AA8 PRO A 226 ASP A 228 5 3 HELIX 9 AA9 LYS A 229 GLY A 234 1 6 HELIX 10 AB1 GLY A 246 GLN A 256 1 11 HELIX 11 AB2 CYS A 259 LYS A 268 1 10 HELIX 12 AB3 GLU B 88 ILE B 92 5 5 HELIX 13 AB4 ILE B 121 ASP B 135 1 15 HELIX 14 AB5 THR B 147 LYS B 165 1 19 HELIX 15 AB6 THR B 168 THR B 178 1 11 HELIX 16 AB7 SER B 186 GLY B 191 5 6 HELIX 17 AB8 THR B 204 SER B 216 1 13 HELIX 18 AB9 TYR B 217 PHE B 219 5 3 HELIX 19 AC1 PRO B 226 ASP B 228 5 3 HELIX 20 AC2 LYS B 229 GLY B 234 1 6 HELIX 21 AC3 GLY B 246 GLY B 257 1 12 HELIX 22 AC4 CYS B 259 GLU B 267 1 9 SHEET 1 AA1 2 LEU A 108 GLN A 110 0 SHEET 2 AA1 2 ARG A 116 ASP A 118 -1 O ILE A 117 N GLU A 109 SHEET 1 AA2 4 PRO A 139 SER A 143 0 SHEET 2 AA2 4 ALA A 193 ALA A 198 -1 O ASP A 195 N SER A 143 SHEET 3 AA2 4 HIS A 241 TYR A 244 -1 O TYR A 242 N VAL A 194 SHEET 4 AA2 4 PHE A 221 ARG A 223 -1 N ILE A 222 O ARG A 243 SHEET 1 AA3 2 LEU B 108 GLN B 110 0 SHEET 2 AA3 2 ARG B 116 ASP B 118 -1 O ILE B 117 N GLU B 109 SHEET 1 AA4 4 PRO B 139 SER B 143 0 SHEET 2 AA4 4 ALA B 193 ALA B 198 -1 O ASP B 195 N SER B 143 SHEET 3 AA4 4 HIS B 241 TYR B 244 -1 O TYR B 242 N VAL B 194 SHEET 4 AA4 4 PHE B 221 ARG B 223 -1 N ILE B 222 O ARG B 243 LINK C ILE A 154 N MSE A 155 1555 1555 1.33 LINK C MSE A 155 N ASP A 156 1555 1555 1.33 LINK N DAL A 302 C DAL A 303 1555 1555 1.37 LINK C ILE B 154 N MSE B 155 1555 1555 1.32 LINK C MSE B 155 N ASP B 156 1555 1555 1.32 LINK N DAL B 302 C DAL B 303 1555 1555 1.36 LINK NE2 HIS A 188 CU CU A 301 1555 1555 2.07 LINK OD1 ASP A 195 CU CU A 301 1555 1555 1.92 LINK ND1 HIS A 241 CU CU A 301 1555 1555 1.99 LINK CU CU A 301 O DAL A 303 1555 1555 1.96 LINK NE2 HIS B 188 CU CU B 301 1555 1555 2.08 LINK OD1 ASP B 195 CU CU B 301 1555 1555 1.94 LINK ND1 HIS B 241 CU CU B 301 1555 1555 1.95 LINK CU CU B 301 O DAL B 303 1555 1555 2.25 SITE 1 AC1 4 HIS A 188 ASP A 195 HIS A 241 DAL A 303 SITE 1 AC2 7 SER A 112 ASN A 113 ARG A 133 ILE A 140 SITE 2 AC2 7 VAL A 141 HOH A 456 GLU B 153 SITE 1 AC3 4 SER A 143 ASP A 195 ASN A 197 TRP A 240 SITE 1 AC4 5 HIS B 188 ASP B 195 HIS B 241 DAL B 302 SITE 2 AC4 5 DAL B 303 SITE 1 AC5 6 GLU A 153 SER B 112 ASN B 113 ARG B 133 SITE 2 AC5 6 ILE B 140 VAL B 141 SITE 1 AC6 3 ASP B 195 ASN B 197 DAL B 303 SITE 1 AC7 12 ARG A 146 GLN A 151 TRP A 179 ALA A 181 SITE 2 AC7 12 SER A 186 HIS A 188 ASP A 195 GLU A 238 SITE 3 AC7 12 TRP A 240 HIS A 241 CU A 301 HOH A 401 SITE 1 AC8 14 ARG B 146 GLN B 151 TRP B 179 VAL B 180 SITE 2 AC8 14 ALA B 181 SER B 186 HIS B 188 ASP B 195 SITE 3 AC8 14 GLU B 238 TRP B 240 HIS B 241 CU B 301 SITE 4 AC8 14 PG4 B 305 HOH B 401 CRYST1 85.861 40.578 115.449 90.00 108.62 90.00 C 1 2 1 8 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 0.011647 0.000000 0.003925 0.00000 SCALE2 0.000000 0.024644 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009140 0.00000