HEADER HYDROLASE 30-APR-16 5G3R TITLE CRYSTAL STRUCTURE OF NAGZ FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH TITLE 2 N-ACETYLGLUCOSAMINE AND L-ALA-1,6-ANHYDROMURNAC COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-HEXOSAMINIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BETA-N-ACETYLHEXOSAMINIDASE,N-ACETYL-BETA-GLUCOSAMINIDASE; COMPND 5 EC: 3.2.1.52; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: CHAIN A CONTAINS A SMALL FRAGMENT (GSH) FROM THE COMPND 8 FUSION TAG USED FOR PURIFICATION, AND CHAIN B CONTAINS ONLY A HIS COMPND 9 RESIDUE AT POSITION -1 FROM THE SAME FUSION TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: PAO1; SOURCE 5 ATCC: 15692; SOURCE 6 GENE: NAGZ, PA3005; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HYDROLASE, CELL-WALL RECYCLING, ANTIBIOTIC RESISTANCE, GLYCOSIDE KEYWDS 2 HYDROLASE, N-ACETYLGLUCOSAMINIDASE, BETA-HEXOSAMINIDASE, KEYWDS 3 PEPTIDOGLYCAN EXPDTA X-RAY DIFFRACTION AUTHOR I.ACEBRON,C.ARTOLA-RECOLONS,K.MAHASENAN,S.MOBASHERY,J.A.HERMOSO REVDAT 5 01-MAY-24 5G3R 1 COMPND SOURCE DBREF SEQADV REVDAT 5 2 1 HETSYN REVDAT 4 29-JUL-20 5G3R 1 COMPND REMARK HETNAM SITE REVDAT 3 31-MAY-17 5G3R 1 JRNL REVDAT 2 24-MAY-17 5G3R 1 JRNL REVDAT 1 17-MAY-17 5G3R 0 JRNL AUTH I.ACEBRON,K.V.MAHASENAN,S.DE BENEDETTI,M.LEE, JRNL AUTH 2 C.ARTOLA-RECOLONS,D.HESEK,H.WANG,J.A.HERMOSO,S.MOBASHERY JRNL TITL CATALYTIC CYCLE OF THE N-ACETYLGLUCOSAMINIDASE NAGZ FROM JRNL TITL 2 PSEUDOMONAS AERUGINOSA. JRNL REF J. AM. CHEM. SOC. V. 139 6795 2017 JRNL REFN ESSN 1520-5126 JRNL PMID 28482153 JRNL DOI 10.1021/JACS.7B01626 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 36197 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1772 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 47.8158 - 5.1241 1.00 2704 157 0.1685 0.1806 REMARK 3 2 5.1241 - 4.0678 1.00 2653 158 0.1552 0.1901 REMARK 3 3 4.0678 - 3.5538 1.00 2647 117 0.1664 0.2312 REMARK 3 4 3.5538 - 3.2290 1.00 2637 156 0.1833 0.2496 REMARK 3 5 3.2290 - 2.9976 1.00 2659 140 0.2252 0.2684 REMARK 3 6 2.9976 - 2.8208 1.00 2666 121 0.2157 0.2647 REMARK 3 7 2.8208 - 2.6796 1.00 2608 137 0.2154 0.2938 REMARK 3 8 2.6796 - 2.5630 1.00 2644 144 0.2222 0.3052 REMARK 3 9 2.5630 - 2.4643 1.00 2647 116 0.2273 0.3072 REMARK 3 10 2.4643 - 2.3793 1.00 2644 121 0.2418 0.3046 REMARK 3 11 2.3793 - 2.3049 1.00 2637 138 0.2397 0.3393 REMARK 3 12 2.3049 - 2.2390 1.00 2637 126 0.2560 0.2991 REMARK 3 13 2.2390 - 2.1800 1.00 2642 141 0.2707 0.3494 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.07 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 : 0.009 5294 REMARK 3 ANGLE : 1.044 7171 REMARK 3 CHIRALITY : 0.055 795 REMARK 3 PLANARITY : 0.006 956 REMARK 3 DIHEDRAL : 18.434 3171 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -3 THROUGH 153 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3996 -7.0540 168.3435 REMARK 3 T TENSOR REMARK 3 T11: 0.2651 T22: 0.2272 REMARK 3 T33: 0.2233 T12: 0.0154 REMARK 3 T13: -0.0087 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 1.9977 L22: 2.6536 REMARK 3 L33: 2.2168 L12: 1.2698 REMARK 3 L13: -0.0270 L23: -0.0640 REMARK 3 S TENSOR REMARK 3 S11: 0.0167 S12: -0.0266 S13: -0.2162 REMARK 3 S21: 0.1138 S22: -0.0696 S23: -0.1640 REMARK 3 S31: 0.1752 S32: -0.1339 S33: 0.0370 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 154 THROUGH 173 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.5036 -11.4200 158.2755 REMARK 3 T TENSOR REMARK 3 T11: 0.4101 T22: 0.2287 REMARK 3 T33: 0.1845 T12: -0.1024 REMARK 3 T13: 0.0503 T23: -0.0481 REMARK 3 L TENSOR REMARK 3 L11: 4.2780 L22: 4.6882 REMARK 3 L33: 2.3330 L12: 0.5645 REMARK 3 L13: 2.7628 L23: 1.9574 REMARK 3 S TENSOR REMARK 3 S11: 0.0462 S12: 0.5813 S13: -0.3395 REMARK 3 S21: -0.4219 S22: -0.0371 S23: 0.1726 REMARK 3 S31: 0.7405 S32: -0.3200 S33: -0.1302 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 174 THROUGH 227 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.7147 -9.0765 152.0350 REMARK 3 T TENSOR REMARK 3 T11: 0.2054 T22: 0.3570 REMARK 3 T33: 0.2590 T12: -0.0800 REMARK 3 T13: -0.0101 T23: -0.0556 REMARK 3 L TENSOR REMARK 3 L11: 3.4569 L22: 3.6869 REMARK 3 L33: 4.5822 L12: 1.6610 REMARK 3 L13: 1.1747 L23: 0.8667 REMARK 3 S TENSOR REMARK 3 S11: -0.1677 S12: 0.3839 S13: -0.0974 REMARK 3 S21: -0.1789 S22: 0.0364 S23: 0.1668 REMARK 3 S31: 0.4060 S32: -0.4702 S33: 0.1616 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 228 THROUGH 332 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.6150 -1.1174 163.2075 REMARK 3 T TENSOR REMARK 3 T11: 0.2161 T22: 0.2321 REMARK 3 T33: 0.2137 T12: 0.0102 REMARK 3 T13: -0.0055 T23: -0.0740 REMARK 3 L TENSOR REMARK 3 L11: 1.6560 L22: 2.3639 REMARK 3 L33: 3.5710 L12: 0.6676 REMARK 3 L13: -0.6432 L23: -1.3507 REMARK 3 S TENSOR REMARK 3 S11: -0.0242 S12: -0.0450 S13: 0.0265 REMARK 3 S21: -0.0748 S22: -0.0388 S23: 0.0545 REMARK 3 S31: -0.1323 S32: -0.1091 S33: 0.1072 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID -1 THROUGH 164 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.6148 -34.1702 168.2328 REMARK 3 T TENSOR REMARK 3 T11: 0.2464 T22: 0.2198 REMARK 3 T33: 0.2121 T12: 0.0148 REMARK 3 T13: -0.0436 T23: 0.0232 REMARK 3 L TENSOR REMARK 3 L11: 2.4903 L22: 2.2719 REMARK 3 L33: 2.1830 L12: 1.1135 REMARK 3 L13: -0.2311 L23: 0.0561 REMARK 3 S TENSOR REMARK 3 S11: -0.0773 S12: -0.0176 S13: 0.2651 REMARK 3 S21: 0.0083 S22: -0.0191 S23: 0.0363 REMARK 3 S31: -0.1814 S32: 0.1473 S33: 0.0673 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 165 THROUGH 242 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.1769 -33.2626 152.9610 REMARK 3 T TENSOR REMARK 3 T11: 0.2934 T22: 0.4561 REMARK 3 T33: 0.4121 T12: -0.1477 REMARK 3 T13: 0.0117 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 2.2829 L22: 4.1602 REMARK 3 L33: 4.6028 L12: 2.2832 REMARK 3 L13: -1.2169 L23: 0.2022 REMARK 3 S TENSOR REMARK 3 S11: -0.2938 S12: 0.3231 S13: 0.0302 REMARK 3 S21: -0.6629 S22: 0.3158 S23: -0.2828 REMARK 3 S31: -0.3450 S32: 0.4967 S33: 0.0742 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 243 THROUGH 332 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.5328 -40.0243 164.1635 REMARK 3 T TENSOR REMARK 3 T11: 0.2051 T22: 0.2690 REMARK 3 T33: 0.2570 T12: 0.0127 REMARK 3 T13: -0.0069 T23: 0.0611 REMARK 3 L TENSOR REMARK 3 L11: 1.4997 L22: 3.3010 REMARK 3 L33: 3.7090 L12: 1.0129 REMARK 3 L13: 0.6321 L23: 1.5505 REMARK 3 S TENSOR REMARK 3 S11: -0.0323 S12: -0.0833 S13: 0.0633 REMARK 3 S21: -0.0926 S22: -0.0398 S23: -0.0599 REMARK 3 S31: 0.0621 S32: -0.0118 S33: 0.1262 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISORDERED REGIONS WERE MODELED REMARK 3 STEREOCHEMICALLY REMARK 4 REMARK 4 5G3R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-APR-16. REMARK 100 THE DEPOSITION ID IS D_1290065948. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97925 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL-CUT REMARK 200 OPTICS : KB MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36231 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 47.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 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) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.90000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: APO STRUCTURE OF NAGZ FROM PSEUDOMONAS AERUGINOSA REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 8000 100 MM SODIUM CACODYLATE REMARK 280 PH 6.0 200 MM SODIUM ACETATE PH 6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 37.31450 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 MET B -20 REMARK 465 GLY B -19 REMARK 465 SER B -18 REMARK 465 SER B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 SER B -10 REMARK 465 SER B -9 REMARK 465 GLY B -8 REMARK 465 LEU B -7 REMARK 465 VAL B -6 REMARK 465 PRO B -5 REMARK 465 ARG B -4 REMARK 465 GLY B -3 REMARK 465 SER B -2 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 OE1 GLU A 185 NH1 ARG A 188 2.16 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 LEU A 7 -168.46 -129.79 REMARK 500 GLU A 38 -75.12 -114.12 REMARK 500 ASN A 89 46.00 -97.19 REMARK 500 ARG A 124 -37.97 -136.43 REMARK 500 VAL A 128 -84.28 -100.28 REMARK 500 GLU A 170 172.03 -54.17 REMARK 500 ASP A 172 70.63 39.35 REMARK 500 SER A 190 -91.27 -135.62 REMARK 500 LEU B 7 -165.71 -128.19 REMARK 500 ARG B 72 -71.33 -112.73 REMARK 500 ASN B 89 44.31 -95.95 REMARK 500 VAL B 128 67.97 -119.26 REMARK 500 SER B 130 4.77 -67.83 REMARK 500 SER B 190 -86.59 -128.22 REMARK 500 ALA B 251 78.23 -58.49 REMARK 500 ASP B 277 88.37 -157.32 REMARK 500 ASN B 309 -179.79 -176.75 REMARK 500 ARG B 313 8.81 -65.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A -1 MET A 1 -147.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2113 DISTANCE = 8.21 ANGSTROMS REMARK 525 HOH B2114 DISTANCE = 7.12 ANGSTROMS REMARK 525 HOH B2115 DISTANCE = 5.84 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 L-ALA-1,6-ANHYDRO-N-ACETYLMURAMIC ACID (89A): THIS REMARK 600 MOLECULES IS ONE OF THE PRODUCTS GENERATED BY THE REMARK 600 HYDROLYSIS OF THE NAG-ANHYDROMUR PENTAPEPTIDE THAT WAS REMARK 600 USED FOR THE SOAKING EXPERIMENTS REMARK 600 N-ACETYL-D-GLUCOSAMINE (NAG): THIS MOLECULES IS ONE OF THE REMARK 600 PRODUCTS GENERATED BY THE HYDROLYSIS OF THE NAG-ANHYDROMUR REMARK 600 PENTAPEPTIDE THAT WAS USED FOR THE SOAKING EXPERIMENTS REMARK 600 DI(HYDROXYETHYL)ETHER (PEG): PEG COMES FROM THE REMARK 600 CRYSTALLIZATION CONDITIONS REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE CONTAINS A HIS-TAG AT THE N-TERMINUS DBREF 5G3R A 1 332 UNP Q9HZK0 NAGZ_PSEAE 1 332 DBREF 5G3R B 1 332 UNP Q9HZK0 NAGZ_PSEAE 1 332 SEQADV 5G3R MET A -20 UNP Q9HZK0 INITIATING METHIONINE SEQADV 5G3R GLY A -19 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R SER A -18 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R SER A -17 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS A -16 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS A -15 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS A -14 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS A -13 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS A -12 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS A -11 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R SER A -10 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R SER A -9 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R GLY A -8 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R LEU A -7 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R VAL A -6 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R PRO A -5 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R ARG A -4 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R GLY A -3 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R SER A -2 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS A -1 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R MET B -20 UNP Q9HZK0 INITIATING METHIONINE SEQADV 5G3R GLY B -19 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R SER B -18 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R SER B -17 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS B -16 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS B -15 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS B -14 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS B -13 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS B -12 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS B -11 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R SER B -10 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R SER B -9 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R GLY B -8 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R LEU B -7 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R VAL B -6 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R PRO B -5 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R ARG B -4 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R GLY B -3 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R SER B -2 UNP Q9HZK0 EXPRESSION TAG SEQADV 5G3R HIS B -1 UNP Q9HZK0 EXPRESSION TAG SEQRES 1 A 352 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 352 LEU VAL PRO ARG GLY SER HIS MET GLN GLY SER LEU MET SEQRES 3 A 352 LEU ASP ILE GLY GLY THR TRP LEU THR ALA GLU ASP ARG SEQRES 4 A 352 GLN ILE LEU ARG HIS PRO GLU VAL GLY GLY LEU ILE ILE SEQRES 5 A 352 PHE ALA ARG ASN ILE GLU HIS PRO ALA GLN VAL ARG GLU SEQRES 6 A 352 LEU CYS ALA ALA ILE ARG ALA ILE ARG PRO ASP LEU LEU SEQRES 7 A 352 LEU ALA VAL ASP GLN GLU GLY GLY ARG VAL GLN ARG LEU SEQRES 8 A 352 ARG GLN GLY PHE VAL ARG LEU PRO ALA MET ARG ALA ILE SEQRES 9 A 352 ALA ASP ASN PRO ASN ALA GLU GLU LEU ALA GLU HIS CYS SEQRES 10 A 352 GLY TRP LEU MET ALA THR GLU VAL GLN ALA VAL GLY LEU SEQRES 11 A 352 ASP LEU SER PHE ALA PRO VAL LEU ASP LEU ASP HIS GLN SEQRES 12 A 352 ARG SER ALA VAL VAL GLY SER ARG ALA PHE GLU GLY ASP SEQRES 13 A 352 PRO GLU ARG ALA ALA LEU LEU ALA GLY ALA PHE ILE ARG SEQRES 14 A 352 GLY MET HIS ALA ALA GLY MET ALA ALA THR GLY LYS HIS SEQRES 15 A 352 PHE PRO GLY HIS GLY TRP ALA GLU ALA ASP SER HIS VAL SEQRES 16 A 352 ALA ILE PRO GLU ASP ALA ARG SER LEU GLU GLU ILE ARG SEQRES 17 A 352 ARG SER ASP LEU VAL PRO PHE ALA ARG LEU ALA GLY GLN SEQRES 18 A 352 LEU ASP ALA LEU MET PRO ALA HIS VAL ILE TYR PRO GLN SEQRES 19 A 352 VAL ASP PRO GLN PRO ALA GLY PHE SER ARG ARG TRP LEU SEQRES 20 A 352 GLN GLU ILE LEU ARG GLY GLU LEU LYS PHE ASP GLY VAL SEQRES 21 A 352 ILE PHE SER ASP ASP LEU SER MET ALA GLY ALA HIS VAL SEQRES 22 A 352 VAL GLY ASP ALA ALA SER ARG ILE GLU ALA ALA LEU ALA SEQRES 23 A 352 ALA GLY CYS ASP MET GLY LEU VAL CYS ASN ASP ARG ALA SEQRES 24 A 352 SER ALA GLU LEU ALA LEU ALA ALA LEU GLN ARG LEU LYS SEQRES 25 A 352 VAL THR PRO PRO SER ARG LEU GLN ARG MET ARG GLY LYS SEQRES 26 A 352 GLY TYR ALA ASN THR ASP TYR ARG GLN GLN PRO ARG TRP SEQRES 27 A 352 LEU GLU ALA LEU SER ALA LEU ARG ALA ALA GLN LEU ILE SEQRES 28 A 352 ASP SEQRES 1 B 352 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 352 LEU VAL PRO ARG GLY SER HIS MET GLN GLY SER LEU MET SEQRES 3 B 352 LEU ASP ILE GLY GLY THR TRP LEU THR ALA GLU ASP ARG SEQRES 4 B 352 GLN ILE LEU ARG HIS PRO GLU VAL GLY GLY LEU ILE ILE SEQRES 5 B 352 PHE ALA ARG ASN ILE GLU HIS PRO ALA GLN VAL ARG GLU SEQRES 6 B 352 LEU CYS ALA ALA ILE ARG ALA ILE ARG PRO ASP LEU LEU SEQRES 7 B 352 LEU ALA VAL ASP GLN GLU GLY GLY ARG VAL GLN ARG LEU SEQRES 8 B 352 ARG GLN GLY PHE VAL ARG LEU PRO ALA MET ARG ALA ILE SEQRES 9 B 352 ALA ASP ASN PRO ASN ALA GLU GLU LEU ALA GLU HIS CYS SEQRES 10 B 352 GLY TRP LEU MET ALA THR GLU VAL GLN ALA VAL GLY LEU SEQRES 11 B 352 ASP LEU SER PHE ALA PRO VAL LEU ASP LEU ASP HIS GLN SEQRES 12 B 352 ARG SER ALA VAL VAL GLY SER ARG ALA PHE GLU GLY ASP SEQRES 13 B 352 PRO GLU ARG ALA ALA LEU LEU ALA GLY ALA PHE ILE ARG SEQRES 14 B 352 GLY MET HIS ALA ALA GLY MET ALA ALA THR GLY LYS HIS SEQRES 15 B 352 PHE PRO GLY HIS GLY TRP ALA GLU ALA ASP SER HIS VAL SEQRES 16 B 352 ALA ILE PRO GLU ASP ALA ARG SER LEU GLU GLU ILE ARG SEQRES 17 B 352 ARG SER ASP LEU VAL PRO PHE ALA ARG LEU ALA GLY GLN SEQRES 18 B 352 LEU ASP ALA LEU MET PRO ALA HIS VAL ILE TYR PRO GLN SEQRES 19 B 352 VAL ASP PRO GLN PRO ALA GLY PHE SER ARG ARG TRP LEU SEQRES 20 B 352 GLN GLU ILE LEU ARG GLY GLU LEU LYS PHE ASP GLY VAL SEQRES 21 B 352 ILE PHE SER ASP ASP LEU SER MET ALA GLY ALA HIS VAL SEQRES 22 B 352 VAL GLY ASP ALA ALA SER ARG ILE GLU ALA ALA LEU ALA SEQRES 23 B 352 ALA GLY CYS ASP MET GLY LEU VAL CYS ASN ASP ARG ALA SEQRES 24 B 352 SER ALA GLU LEU ALA LEU ALA ALA LEU GLN ARG LEU LYS SEQRES 25 B 352 VAL THR PRO PRO SER ARG LEU GLN ARG MET ARG GLY LYS SEQRES 26 B 352 GLY TYR ALA ASN THR ASP TYR ARG GLN GLN PRO ARG TRP SEQRES 27 B 352 LEU GLU ALA LEU SER ALA LEU ARG ALA ALA GLN LEU ILE SEQRES 28 B 352 ASP HET NAG A1333 15 HET 89A A1334 24 HET PEG B1333 7 HET PEG B1334 7 HET NAG B1335 15 HET 89A B1336 24 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM 89A 2-[[(2R)-2-[[(1R,2S,3R,4R,5R)-4-ACETAMIDO-2-OXIDANYL-6, HETNAM 2 89A 8-DIOXABICYCLO[3.2.1]OCTAN-3- HETNAM 3 89A YL]OXY]PROPANOYL]AMINO]PROPANAMIDE HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 NAG 2(C8 H15 N O6) FORMUL 4 89A 2(C14 H23 N3 O7) FORMUL 5 PEG 2(C4 H10 O3) FORMUL 9 HOH *253(H2 O) HELIX 1 1 THR A 15 ARG A 23 1 9 HELIX 2 2 PHE A 33 ILE A 37 5 5 HELIX 3 3 HIS A 39 ARG A 54 1 16 HELIX 4 4 ALA A 80 ASP A 86 1 7 HELIX 5 5 ASN A 89 VAL A 108 1 20 HELIX 6 6 VAL A 128 ALA A 132 5 5 HELIX 7 7 ASP A 136 ALA A 154 1 19 HELIX 8 8 SER A 183 ARG A 189 1 7 HELIX 9 9 LEU A 192 ALA A 199 1 8 HELIX 10 10 ALA A 220 PHE A 222 5 3 HELIX 11 11 SER A 223 GLN A 228 1 6 HELIX 12 12 GLU A 229 LEU A 235 1 7 HELIX 13 13 ASP A 256 GLY A 268 1 13 HELIX 14 14 ASP A 277 LEU A 291 1 15 HELIX 15 15 PRO A 296 ARG A 303 5 8 HELIX 16 16 ASP A 311 GLN A 314 5 4 HELIX 17 17 GLN A 315 ALA A 328 1 14 HELIX 18 18 THR B 15 ARG B 23 1 9 HELIX 19 19 PHE B 33 ILE B 37 5 5 HELIX 20 20 HIS B 39 ARG B 54 1 16 HELIX 21 21 ALA B 80 ASP B 86 1 7 HELIX 22 22 ASN B 89 VAL B 108 1 20 HELIX 23 23 ASP B 136 ALA B 154 1 19 HELIX 24 24 SER B 183 SER B 190 1 8 HELIX 25 25 LEU B 192 ALA B 199 1 8 HELIX 26 26 SER B 223 GLN B 228 1 6 HELIX 27 27 GLU B 229 LEU B 235 1 7 HELIX 28 28 ASP B 256 GLY B 268 1 13 HELIX 29 29 ASP B 277 LYS B 292 1 16 HELIX 30 30 PRO B 296 ARG B 303 5 8 HELIX 31 31 ASP B 311 GLN B 314 5 4 HELIX 32 32 GLN B 315 ALA B 328 1 14 SHEET 1 AA 8 LEU A 112 SER A 113 0 SHEET 2 AA 8 LEU A 58 VAL A 61 1 O LEU A 59 N LEU A 112 SHEET 3 AA 8 VAL A 27 ILE A 31 1 O GLY A 28 N LEU A 58 SHEET 4 AA 8 SER A 4 LEU A 7 1 O LEU A 5 N GLY A 28 SHEET 5 AA 8 MET A 271 LEU A 273 1 O GLY A 272 N MET A 6 SHEET 6 AA 8 VAL A 240 ASP A 245 1 N SER A 243 O MET A 271 SHEET 7 AA 8 ALA A 204 PRO A 207 1 O LEU A 205 N PHE A 242 SHEET 8 AA 8 THR A 159 PHE A 163 1 O GLY A 160 N MET A 206 SHEET 1 AB 2 GLN A 63 GLY A 65 0 SHEET 2 AB 2 VAL A 68 GLN A 69 -1 O VAL A 68 N GLY A 65 SHEET 1 BA 8 LEU B 112 SER B 113 0 SHEET 2 BA 8 LEU B 58 VAL B 61 1 N VAL B 61 O LEU B 112 SHEET 3 BA 8 VAL B 27 ILE B 32 1 O GLY B 28 N LEU B 58 SHEET 4 BA 8 SER B 4 LEU B 7 1 O LEU B 5 N GLY B 28 SHEET 5 BA 8 MET B 271 LEU B 273 1 O GLY B 272 N MET B 6 SHEET 6 BA 8 VAL B 240 ASP B 245 1 N SER B 243 O MET B 271 SHEET 7 BA 8 ALA B 204 PRO B 207 1 O LEU B 205 N PHE B 242 SHEET 8 BA 8 THR B 159 PHE B 163 1 O GLY B 160 N MET B 206 SHEET 1 BB 2 GLN B 63 GLY B 65 0 SHEET 2 BB 2 VAL B 68 GLN B 69 -1 O VAL B 68 N GLY B 65 SHEET 1 BC 2 ILE B 211 TYR B 212 0 SHEET 2 BC 2 ASP B 216 PRO B 219 -1 O ASP B 216 N TYR B 212 CISPEP 1 ALA A 115 PRO A 116 0 7.49 CISPEP 2 LYS A 161 HIS A 162 0 4.75 CISPEP 3 PHE A 163 PRO A 164 0 1.34 CISPEP 4 ALA B 115 PRO B 116 0 3.99 CISPEP 5 LYS B 161 HIS B 162 0 3.70 CISPEP 6 PHE B 163 PRO B 164 0 -0.07 CRYST1 66.657 74.629 75.560 90.00 110.94 90.00 P 1 21 1 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 0.015002 0.000000 0.005741 0.00000 SCALE2 0.000000 0.013400 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014170 0.00000