HEADER HYDROLASE 05-FEB-16 5I1T TITLE 2.6 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF STAGE II SPORULATION TITLE 2 PROTEIN D (SPOIID) FROM CLOSTRIDIUM DIFFICILE IN COMPLEX WITH TITLE 3 TRIACETYLCHITOTRIOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: STAGE II SPORULATION PROTEIN D; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PEPTOCLOSTRIDIUM DIFFICILE (STRAIN 630); SOURCE 3 ORGANISM_TAXID: 272563; SOURCE 4 STRAIN: 630; SOURCE 5 GENE: SPOIID, CD630_01240; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG53 KEYWDS SPOIID, TRIACETYLCHITOTRIOSE, STRUCTURAL GENOMICS, CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.NOCADELLO,G.MINASOV,L.SHUVALOVA,I.DUBROVSKA,S.GRIMSHAW,K.KWON, AUTHOR 2 W.F.ANDERSON,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES AUTHOR 3 (CSGID) REVDAT 5 27-SEP-23 5I1T 1 HETSYN REVDAT 4 29-JUL-20 5I1T 1 COMPND JRNL REMARK HET REVDAT 4 2 1 HETNAM HETSYN FORMUL LINK REVDAT 4 3 1 SITE ATOM REVDAT 3 27-JUL-16 5I1T 1 JRNL REVDAT 2 08-JUN-16 5I1T 1 JRNL REVDAT 1 25-MAY-16 5I1T 0 JRNL AUTH S.NOCADELLO,G.MINASOV,L.S.SHUVALOVA,I.DUBROVSKA,E.SABINI, JRNL AUTH 2 W.F.ANDERSON JRNL TITL CRYSTAL STRUCTURES OF THE SPOIID LYTIC TRANSGLYCOSYLASES JRNL TITL 2 ESSENTIAL FOR BACTERIAL SPORULATION. JRNL REF J.BIOL.CHEM. V. 291 14915 2016 JRNL REFN ESSN 1083-351X JRNL PMID 27226615 JRNL DOI 10.1074/JBC.M116.729749 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17967 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 976 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1285 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2280 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 95 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 69.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.92000 REMARK 3 B22 (A**2) : -0.92000 REMARK 3 B33 (A**2) : 2.97000 REMARK 3 B12 (A**2) : -0.46000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.235 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.196 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.413 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2466 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2318 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3325 ; 1.477 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5390 ; 0.853 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 292 ; 2.939 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;33.644 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 449 ;10.446 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;11.809 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 372 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2704 ; 0.023 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 538 ; 0.019 ; 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): 1159 ; 2.416 ; 4.409 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1158 ; 2.416 ; 4.409 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1454 ; 3.610 ; 6.614 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1455 ; 3.608 ; 6.614 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1307 ; 4.271 ; 5.214 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1307 ; 4.224 ; 5.215 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1872 ; 6.701 ; 7.627 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2781 ; 8.781 ;36.696 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2743 ; 8.729 ;36.335 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 70 A 152 REMARK 3 ORIGIN FOR THE GROUP (A): -62.5966 2.6717 -0.5129 REMARK 3 T TENSOR REMARK 3 T11: 0.3635 T22: 0.1539 REMARK 3 T33: 0.2000 T12: -0.0303 REMARK 3 T13: 0.1140 T23: -0.0403 REMARK 3 L TENSOR REMARK 3 L11: 3.4963 L22: 1.9720 REMARK 3 L33: 2.9482 L12: -0.7650 REMARK 3 L13: -0.2189 L23: -0.9181 REMARK 3 S TENSOR REMARK 3 S11: 0.0824 S12: 0.1131 S13: 0.1617 REMARK 3 S21: 0.1532 S22: 0.0609 S23: 0.4837 REMARK 3 S31: -0.4217 S32: -0.5344 S33: -0.1433 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 153 A 221 REMARK 3 ORIGIN FOR THE GROUP (A): -53.9281 -1.8155 0.4220 REMARK 3 T TENSOR REMARK 3 T11: 0.2651 T22: 0.0403 REMARK 3 T33: 0.0672 T12: -0.0595 REMARK 3 T13: 0.0678 T23: -0.0458 REMARK 3 L TENSOR REMARK 3 L11: 2.4505 L22: 2.2738 REMARK 3 L33: 3.3606 L12: 0.6188 REMARK 3 L13: -1.0250 L23: -0.0736 REMARK 3 S TENSOR REMARK 3 S11: 0.1828 S12: 0.0373 S13: 0.0674 REMARK 3 S21: 0.1731 S22: -0.1127 S23: 0.2021 REMARK 3 S31: -0.1932 S32: -0.0913 S33: -0.0701 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 222 A 290 REMARK 3 ORIGIN FOR THE GROUP (A): -36.3810 16.1037 -13.1754 REMARK 3 T TENSOR REMARK 3 T11: 0.2305 T22: 0.1301 REMARK 3 T33: 0.0606 T12: -0.1055 REMARK 3 T13: 0.0521 T23: -0.0490 REMARK 3 L TENSOR REMARK 3 L11: 1.3708 L22: 4.1758 REMARK 3 L33: 0.6663 L12: 0.3640 REMARK 3 L13: -0.2139 L23: 0.0963 REMARK 3 S TENSOR REMARK 3 S11: 0.1425 S12: -0.0540 S13: 0.1815 REMARK 3 S21: -0.1339 S22: -0.0921 S23: 0.1195 REMARK 3 S31: -0.1784 S32: 0.2520 S33: -0.0504 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 291 A 354 REMARK 3 ORIGIN FOR THE GROUP (A): -43.4808 1.0318 -3.2395 REMARK 3 T TENSOR REMARK 3 T11: 0.3357 T22: 0.1387 REMARK 3 T33: 0.0548 T12: -0.1076 REMARK 3 T13: 0.0406 T23: -0.0658 REMARK 3 L TENSOR REMARK 3 L11: 1.8399 L22: 1.6588 REMARK 3 L33: 1.7518 L12: 1.1316 REMARK 3 L13: -1.2824 L23: -1.1052 REMARK 3 S TENSOR REMARK 3 S11: 0.1474 S12: -0.1758 S13: 0.0165 REMARK 3 S21: 0.1535 S22: -0.1596 S23: 0.0355 REMARK 3 S31: -0.0633 S32: 0.2643 S33: 0.0123 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5I1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218113. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : BERYLLIUM LENSES REMARK 200 OPTICS : C(111) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18969 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 30.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.30 REMARK 200 R MERGE FOR SHELL (I) : 0.60800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 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: PDB-4RWR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 7.0 MG/ML, 0.5M SODIUM REMARK 280 CHLORIDE, 0.01M TRIS-HCL (PH 7.2), 2MM NAG3, 1/100 ELOSTASE; REMARK 280 SCREEN: JCSG+ (B11), 1.6M TRI-SODIUM CITRATE PH 6.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 36.10900 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 72.21800 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 72.21800 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 36.10900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A 25 REMARK 465 ASN A 26 REMARK 465 ALA A 27 REMARK 465 LYS A 28 REMARK 465 ASN A 29 REMARK 465 VAL A 30 REMARK 465 GLU A 31 REMARK 465 LEU A 32 REMARK 465 THR A 33 REMARK 465 GLU A 34 REMARK 465 LYS A 35 REMARK 465 PRO A 36 REMARK 465 GLU A 37 REMARK 465 SER A 38 REMARK 465 PRO A 39 REMARK 465 VAL A 40 REMARK 465 SER A 41 REMARK 465 ILE A 42 REMARK 465 ASN A 43 REMARK 465 LYS A 44 REMARK 465 THR A 45 REMARK 465 ILE A 46 REMARK 465 LYS A 47 REMARK 465 LYS A 48 REMARK 465 SER A 49 REMARK 465 ASP A 50 REMARK 465 ILE A 51 REMARK 465 GLU A 52 REMARK 465 ASP A 53 REMARK 465 LYS A 54 REMARK 465 GLY A 55 REMARK 465 ASN A 56 REMARK 465 LYS A 57 REMARK 465 GLU A 58 REMARK 465 GLU A 59 REMARK 465 LYS A 60 REMARK 465 ASN A 61 REMARK 465 THR A 62 REMARK 465 VAL A 63 REMARK 465 ASN A 64 REMARK 465 TYR A 65 REMARK 465 GLU A 66 REMARK 465 THR A 67 REMARK 465 VAL A 68 REMARK 465 ASN A 69 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 OG SER A 221 OD1 ASP A 224 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O7 NAG C 2 O7 NAG C 2 5554 2.19 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 CYS A 146 -88.40 -116.83 REMARK 500 PHE A 209 -123.91 -109.10 REMARK 500 LEU A 216 66.15 -109.64 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 134 NE2 REMARK 620 2 CYS A 140 SG 96.4 REMARK 620 3 HIS A 145 ND1 96.8 116.3 REMARK 620 4 CYS A 146 SG 113.6 124.0 106.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 179 O REMARK 620 2 LYS A 261 O 39.3 REMARK 620 3 ASP A 352 OD2 98.2 70.4 REMARK 620 4 TYR A 354 O 101.1 97.2 129.1 REMARK 620 5 HOH A 572 O 101.2 134.4 105.1 116.4 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: CSGID-IDP05616 RELATED DB: TARGETTRACK DBREF 5I1T A 28 354 UNP Q18CL6 Q18CL6_PEPD6 28 354 SEQADV 5I1T SER A 25 UNP Q18CL6 EXPRESSION TAG SEQADV 5I1T ASN A 26 UNP Q18CL6 EXPRESSION TAG SEQADV 5I1T ALA A 27 UNP Q18CL6 EXPRESSION TAG SEQRES 1 A 330 SER ASN ALA LYS ASN VAL GLU LEU THR GLU LYS PRO GLU SEQRES 2 A 330 SER PRO VAL SER ILE ASN LYS THR ILE LYS LYS SER ASP SEQRES 3 A 330 ILE GLU ASP LYS GLY ASN LYS GLU GLU LYS ASN THR VAL SEQRES 4 A 330 ASN TYR GLU THR VAL ASN LYS LYS ALA PRO ILE ILE ASN SEQRES 5 A 330 VAL TYR ASN HIS ILE THR GLY LYS THR GLU LYS MET ASP SEQRES 6 A 330 MET GLU ASN TYR LEU CYS GLY VAL LEU ALA GLY GLU MET SEQRES 7 A 330 SER SER GLU PHE ASP ILE GLU ALA LEU LYS ALA GLN SER SEQRES 8 A 330 VAL ALA ALA ARG THR TYR VAL VAL TYR LYS GLN GLU HIS SEQRES 9 A 330 GLY LYS SER SER LYS HIS LYS ASN ALA VAL VAL CYS THR SEQRES 10 A 330 ASP TYR LYS HIS CYS GLN GLU TYR LYS SER TYR ASP THR SEQRES 11 A 330 LEU LYS LYS LEU ASN GLY GLU GLU TRP ILE LYS ASN LYS SEQRES 12 A 330 TYR SER LYS ILE GLN GLU ALA VAL ARG GLY THR LYS GLY SEQRES 13 A 330 GLN ILE ILE THR TYR ASN ASP LYS ALA ILE LEU PRO LEU SEQRES 14 A 330 TYR PHE SER THR SER SER GLY LYS THR GLU ASN SER GLU SEQRES 15 A 330 GLU VAL PHE SER ALA LYS TYR PRO TYR LEU LYS SER VAL SEQRES 16 A 330 GLU SER PRO TYR ASP LYS TYR SER PRO LYS PHE ALA SER SEQRES 17 A 330 THR LEU LYS ILE SER ASN THR ASP PHE VAL LYS SER LEU SEQRES 18 A 330 ARG ARG ALA TYR SER THR ILE VAL ILE ASP VAL ASN ASN SEQRES 19 A 330 LEU SER LYS GLN VAL SER ILE THR LYS ARG SER ASP ALA SEQRES 20 A 330 GLY THR VAL GLU LYS ILE LYS LEU GLY ASN LYS GLU LEU SEQRES 21 A 330 THR GLY LYS ASP ILE ARG THR VAL PHE LYS LEU ASN SER SEQRES 22 A 330 ALA ASN PHE ASP ILE LYS PHE GLY GLU GLY TYR ILE ASP SEQRES 23 A 330 PHE VAL VAL LYS GLY TYR GLY HIS GLY VAL GLY MET SER SEQRES 24 A 330 GLN TRP GLY ALA GLU GLY MET ALA GLU GLU GLY TYR LYS SEQRES 25 A 330 TYR TYR ASP ILE LEU SER HIS TYR TYR THR ASP THR LYS SEQRES 26 A 330 ILE LYS ASP ILE TYR HET NAG B 1 15 HET NAG B 2 14 HET NAG B 3 14 HET NAG C 1 15 HET NAG C 2 14 HET NAG C 3 14 HET ZN A 401 1 HET NA A 402 1 HET CL A 403 1 HET GOL A 406 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL 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 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAG 6(C8 H15 N O6) FORMUL 4 ZN ZN 2+ FORMUL 5 NA NA 1+ FORMUL 6 CL CL 1- FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *147(H2 O) HELIX 1 AA1 MET A 90 MET A 102 1 13 HELIX 2 AA2 ASP A 107 HIS A 128 1 22 HELIX 3 AA3 SER A 151 GLY A 160 1 10 HELIX 4 AA4 GLY A 160 LYS A 167 1 8 HELIX 5 AA5 LYS A 167 THR A 178 1 12 HELIX 6 AA6 ASN A 204 PHE A 209 1 6 HELIX 7 AA7 TYR A 223 SER A 227 5 5 HELIX 8 AA8 ASN A 238 TYR A 249 1 12 HELIX 9 AA9 ASN A 258 LYS A 261 5 4 HELIX 10 AB1 THR A 285 LYS A 294 1 10 HELIX 11 AB2 GLN A 324 GLU A 333 1 10 HELIX 12 AB3 LYS A 336 TYR A 345 1 10 SHEET 1 AA1 3 LYS A 84 ASP A 89 0 SHEET 2 AA1 3 ILE A 74 ASN A 79 -1 N ILE A 75 O MET A 88 SHEET 3 AA1 3 VAL A 139 CYS A 140 1 O VAL A 139 N TYR A 78 SHEET 1 AA2 3 LYS A 188 ALA A 189 0 SHEET 2 AA2 3 GLN A 181 TYR A 185 -1 N TYR A 185 O LYS A 188 SHEET 3 AA2 3 LYS A 349 ASP A 352 -1 O LYS A 351 N ILE A 182 SHEET 1 AA3 2 TYR A 194 PHE A 195 0 SHEET 2 AA3 2 MET A 322 SER A 323 1 O MET A 322 N PHE A 195 SHEET 1 AA4 3 ALA A 231 SER A 237 0 SHEET 2 AA4 3 TYR A 308 LYS A 314 -1 O PHE A 311 N LEU A 234 SHEET 3 AA4 3 PHE A 300 PHE A 304 -1 N LYS A 303 O ASP A 310 SHEET 1 AA5 3 VAL A 263 ARG A 268 0 SHEET 2 AA5 3 VAL A 274 LEU A 279 -1 O LYS A 278 N SER A 264 SHEET 3 AA5 3 LYS A 282 LEU A 284 -1 O LYS A 282 N LEU A 279 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.43 LINK O4 NAG B 2 C1 NAG B 3 1555 1555 1.43 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG C 2 C1 NAG C 3 1555 1555 1.43 LINK NE2 HIS A 134 ZN ZN A 401 1555 1555 2.19 LINK SG CYS A 140 ZN ZN A 401 1555 1555 2.33 LINK ND1 HIS A 145 ZN ZN A 401 1555 1555 2.15 LINK SG CYS A 146 ZN ZN A 401 1555 1555 2.34 LINK O LYS A 179 NA NA A 402 1555 1555 2.24 LINK O LYS A 261 NA NA A 402 1555 4565 2.37 LINK OD2 ASP A 352 NA NA A 402 1555 1555 2.29 LINK O TYR A 354 NA NA A 402 1555 1555 2.25 LINK NA NA A 402 O HOH A 572 1555 4455 2.42 CRYST1 98.082 98.082 108.327 90.00 90.00 120.00 P 31 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 0.010196 0.005886 0.000000 0.00000 SCALE2 0.000000 0.011773 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009231 0.00000