HEADER HYDROLASE 23-APR-14 4Q6Q TITLE STRUCTURAL ANALYSIS OF THE ZN-FORM II OF HELICOBACTER PYLORI CSD4, A TITLE 2 D,L-CARBOXYPEPTIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONSERVED HYPOTHETICAL SECRETED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 22-438; COMPND 5 SYNONYM: CSD4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 85962; SOURCE 4 STRAIN: ATCC 700392; SOURCE 5 GENE: HP_1075; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS M14 METALLOPEPTIDASE, D, L-CARBOXYPEPTIDASE, PEPTIDOGLYCAN, CSD5, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.S.KIM,J.KIM,H.N.IM,D.R.AN,M.LEE,D.HESEK,S.MOBASHERY,J.Y.KIM,K.CHO, AUTHOR 2 H.J.YOON,B.W.HAN,B.I.LEE,S.W.SUH REVDAT 3 15-NOV-23 4Q6Q 1 REMARK SEQADV LINK ATOM REVDAT 2 19-NOV-14 4Q6Q 1 JRNL REVDAT 1 05-NOV-14 4Q6Q 0 JRNL AUTH H.S.KIM,J.KIM,H.N.IM,D.R.AN,M.LEE,D.HESEK,S.MOBASHERY, JRNL AUTH 2 J.Y.KIM,K.CHO,H.J.YOON,B.W.HAN,B.I.LEE,S.W.SUH JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION OF MURAMYLTRIPEPTIDE BY JRNL TITL 2 HELICOBACTER PYLORI CSD4, A D,L-CARBOXYPEPTIDASE CONTROLLING JRNL TITL 3 THE HELICAL CELL SHAPE JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 2800 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 25372672 JRNL DOI 10.1107/S1399004714018732 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 19704 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1066 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1336 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE SET COUNT : 69 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3366 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 223 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.85000 REMARK 3 B22 (A**2) : -0.64000 REMARK 3 B33 (A**2) : -1.21000 REMARK 3 B12 (A**2) : 0.00000 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): 0.337 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.215 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.448 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3459 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3374 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4676 ; 1.338 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7774 ; 0.768 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 416 ; 6.568 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;36.352 ;24.880 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 621 ;14.634 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;14.325 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 507 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3902 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 799 ; 0.001 ; 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): 1667 ; 1.687 ; 3.078 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1666 ; 1.680 ; 3.077 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2082 ; 2.687 ; 4.614 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2083 ; 2.689 ; 4.615 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1792 ; 2.194 ; 3.393 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1793 ; 2.193 ; 3.393 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2595 ; 3.623 ; 4.970 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3876 ; 5.197 ;24.854 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3876 ; 5.196 ;24.854 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 4Q6Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085673. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2823 REMARK 200 MONOCHROMATOR : DCM SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38851 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 10.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M CALCIUM CHLORIDE, 0.1M HEPES REMARK 280 -NAOH, 25%(W/V) POLYETHYLENE GLYCOL 3350, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 26.65700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.40300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.46400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.40300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.65700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.46400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 SER A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 HIS A 11 REMARK 465 SER A 12 REMARK 465 SER A 13 REMARK 465 GLY A 14 REMARK 465 LEU A 15 REMARK 465 VAL A 16 REMARK 465 PRO A 17 REMARK 465 ARG A 18 REMARK 465 GLY A 19 REMARK 465 SER A 20 REMARK 465 HIS A 21 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 O HOH A 766 O HOH A 805 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 ALA A 97 -116.86 -109.17 REMARK 500 GLN A 198 35.76 -80.13 REMARK 500 ASN A 267 50.56 -102.02 REMARK 500 SER A 276 -129.75 46.61 REMARK 500 LYS A 319 -120.07 61.15 REMARK 500 ASP A 353 61.63 34.60 REMARK 500 ASN A 354 -15.64 81.52 REMARK 500 GLU A 369 -49.61 -130.14 REMARK 500 ASN A 378 -9.36 73.88 REMARK 500 ASN A 426 -122.49 62.89 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 CA A 504 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 173 OD1 REMARK 620 2 GLU A 176 OE1 84.1 REMARK 620 3 GLU A 176 OE2 77.1 47.5 REMARK 620 4 HOH A 674 O 74.7 149.8 141.8 REMARK 620 5 HOH A 773 O 86.7 76.4 122.4 81.0 REMARK 620 6 HOH A 787 O 155.7 77.6 78.7 128.0 104.2 REMARK 620 7 HOH A 813 O 132.3 130.0 149.7 59.7 73.7 72.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 382 OD1 REMARK 620 2 VAL A 383 O 90.7 REMARK 620 3 PHE A 386 O 168.8 78.3 REMARK 620 4 GLU A 396 OE2 100.8 128.2 84.4 REMARK 620 5 GLU A 396 OE1 85.5 80.1 90.2 51.3 REMARK 620 6 HOH A 636 O 100.7 82.1 80.4 142.2 161.3 REMARK 620 7 HOH A 665 O 93.5 152.0 97.4 78.1 127.8 69.9 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE API A 505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Q6M RELATED DB: PDB REMARK 900 RELATED ID: 4Q6N RELATED DB: PDB REMARK 900 RELATED ID: 4Q6O RELATED DB: PDB REMARK 900 RELATED ID: 4Q6P RELATED DB: PDB DBREF 4Q6Q A 22 438 UNP O25708 O25708_HELPY 22 438 SEQADV 4Q6Q MET A 2 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q GLY A 3 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q SER A 4 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q SER A 5 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q HIS A 6 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q HIS A 7 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q HIS A 8 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q HIS A 9 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q HIS A 10 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q HIS A 11 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q SER A 12 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q SER A 13 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q GLY A 14 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q LEU A 15 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q VAL A 16 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q PRO A 17 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q ARG A 18 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q GLY A 19 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q SER A 20 UNP O25708 EXPRESSION TAG SEQADV 4Q6Q HIS A 21 UNP O25708 EXPRESSION TAG SEQRES 1 A 437 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 437 LEU VAL PRO ARG GLY SER HIS MET ILE GLU LYS ALA PRO SEQRES 3 A 437 THR ASN VAL GLU ASP ARG ASP LYS ALA PRO HIS LEU LEU SEQRES 4 A 437 LEU LEU ALA GLY ILE GLN GLY ASP GLU PRO GLY GLY PHE SEQRES 5 A 437 ASN ALA THR ASN LEU PHE LEU MET HIS TYR SER VAL LEU SEQRES 6 A 437 LYS GLY LEU VAL GLU VAL VAL PRO VAL LEU ASN LYS PRO SEQRES 7 A 437 SER MET LEU ARG ASN HIS ARG GLY LEU TYR GLY ASP MET SEQRES 8 A 437 ASN ARG LYS PHE ALA ALA LEU ASP LYS ASN ASP PRO GLU SEQRES 9 A 437 TYR PRO THR ILE GLN GLU ILE LYS SER LEU ILE ALA LYS SEQRES 10 A 437 PRO SER ILE ASP ALA VAL LEU HIS LEU HIS ASP GLY GLY SEQRES 11 A 437 GLY TYR TYR ARG PRO VAL TYR VAL ASP ALA MET LEU ASN SEQRES 12 A 437 PRO LYS ARG TRP GLY ASN CYS PHE ILE ILE ASP GLN ASP SEQRES 13 A 437 GLU VAL LYS GLY ALA LYS PHE PRO ASN LEU LEU ALA PHE SEQRES 14 A 437 ALA ASN ASN THR ILE GLU SER ILE ASN ALA HIS LEU LEU SEQRES 15 A 437 HIS PRO ILE GLU GLU TYR HIS LEU LYS ASN THR ARG THR SEQRES 16 A 437 ALA GLN GLY ASP THR GLU MET GLN LYS ALA LEU THR PHE SEQRES 17 A 437 TYR ALA ILE ASN GLN LYS LYS SER ALA PHE ALA ASN GLU SEQRES 18 A 437 ALA SER LYS GLU LEU PRO LEU ALA SER ARG VAL PHE TYR SEQRES 19 A 437 HIS LEU GLN ALA ILE GLU GLY LEU LEU ASN GLN LEU ASN SEQRES 20 A 437 ILE PRO PHE LYS ARG ASP PHE ASP LEU ASN PRO ASN SER SEQRES 21 A 437 VAL HIS ALA LEU ILE ASN ASP LYS ASN LEU TRP ALA LYS SEQRES 22 A 437 ILE SER SER LEU PRO LYS MET PRO LEU PHE ASN LEU ARG SEQRES 23 A 437 PRO LYS LEU ASN HIS PHE PRO LEU PRO HIS ASN THR LYS SEQRES 24 A 437 ILE PRO GLN ILE PRO ILE GLU SER ASN ALA TYR ILE VAL SEQRES 25 A 437 GLY LEU VAL LYS ASN LYS GLN GLU VAL PHE LEU LYS TYR SEQRES 26 A 437 GLY ASN LYS LEU MET THR ARG LEU SER PRO PHE TYR ILE SEQRES 27 A 437 GLU PHE ASP PRO SER LEU GLU GLU VAL LYS MET GLN ILE SEQRES 28 A 437 ASP ASN LYS ASP GLN MET VAL LYS ILE GLY SER VAL VAL SEQRES 29 A 437 GLU VAL LYS GLU SER PHE TYR ILE HIS ALA MET ASP ASN SEQRES 30 A 437 ILE ARG ALA ASN VAL ILE GLY PHE SER VAL SER ASN GLU SEQRES 31 A 437 ASN LYS PRO ASN GLU ALA GLY TYR THR ILE LYS PHE LYS SEQRES 32 A 437 ASP PHE GLN LYS ARG PHE SER LEU ASP LYS GLN GLU ARG SEQRES 33 A 437 ILE TYR ARG ILE GLU PHE TYR LYS ASN ASN ALA PHE SER SEQRES 34 A 437 GLY MET ILE LEU VAL LYS PHE VAL HET ZN A 501 1 HET ZN A 502 1 HET CA A 503 1 HET CA A 504 1 HET API A 505 13 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM API 2,6-DIAMINOPIMELIC ACID FORMUL 2 ZN 2(ZN 2+) FORMUL 4 CA 2(CA 2+) FORMUL 6 API C7 H14 N2 O4 FORMUL 7 HOH *223(H2 O) HELIX 1 1 ASN A 29 ALA A 36 5 8 HELIX 2 2 GLU A 49 HIS A 62 1 14 HELIX 3 3 ASN A 77 ARG A 83 1 7 HELIX 4 4 ASP A 91 LYS A 95 5 5 HELIX 5 5 GLU A 105 LYS A 118 1 14 HELIX 6 6 ASN A 166 ALA A 180 1 15 HELIX 7 7 HIS A 184 GLU A 188 5 5 HELIX 8 8 ARG A 195 GLY A 199 5 5 HELIX 9 9 GLU A 202 LYS A 205 5 4 HELIX 10 10 ALA A 206 GLN A 214 1 9 HELIX 11 11 PRO A 228 ASN A 248 1 21 HELIX 12 12 ASN A 258 ASN A 267 1 10 HELIX 13 13 LYS A 300 ILE A 304 5 5 HELIX 14 14 LYS A 404 PHE A 406 5 3 HELIX 15 15 GLN A 407 SER A 411 5 5 SHEET 1 A 7 ILE A 23 LYS A 25 0 SHEET 2 A 7 LEU A 69 VAL A 73 -1 O VAL A 72 N ILE A 23 SHEET 3 A 7 HIS A 38 LEU A 42 1 N LEU A 41 O GLU A 71 SHEET 4 A 7 ALA A 123 GLY A 130 1 O LEU A 125 N LEU A 42 SHEET 5 A 7 SER A 217 SER A 224 1 O ASN A 221 N HIS A 128 SHEET 6 A 7 CYS A 151 ILE A 154 -1 N ILE A 153 O ALA A 220 SHEET 7 A 7 HIS A 190 ASN A 193 1 O LYS A 192 N PHE A 152 SHEET 1 B 2 TYR A 63 VAL A 65 0 SHEET 2 B 2 PHE A 251 ARG A 253 -1 O LYS A 252 N SER A 64 SHEET 1 C 2 TYR A 133 TYR A 134 0 SHEET 2 C 2 LEU A 143 ASN A 144 1 O ASN A 144 N TYR A 133 SHEET 1 D 3 MET A 281 PRO A 282 0 SHEET 2 D 3 TRP A 272 ILE A 275 -1 N ALA A 273 O MET A 281 SHEET 3 D 3 ILE A 306 SER A 308 -1 O GLU A 307 N LYS A 274 SHEET 1 E 4 LYS A 289 PRO A 296 0 SHEET 2 E 4 LYS A 329 PHE A 341 1 O SER A 335 N LEU A 290 SHEET 3 E 4 ALA A 428 PHE A 437 1 O PHE A 429 N GLU A 340 SHEET 4 E 4 VAL A 364 VAL A 367 1 N VAL A 367 O LYS A 436 SHEET 1 F 6 VAL A 313 ASN A 318 0 SHEET 2 F 6 GLU A 321 TYR A 326 -1 O PHE A 323 N VAL A 316 SHEET 3 F 6 LYS A 329 PHE A 341 -1 O MET A 331 N LEU A 324 SHEET 4 F 6 ALA A 428 PHE A 437 1 O PHE A 429 N GLU A 340 SHEET 5 F 6 ILE A 418 LYS A 425 -1 N PHE A 423 O SER A 430 SHEET 6 F 6 ARG A 380 VAL A 383 -1 N ASN A 382 O GLU A 422 SHEET 1 G 4 LYS A 355 LYS A 360 0 SHEET 2 G 4 GLU A 347 ILE A 352 -1 N VAL A 348 O VAL A 359 SHEET 3 G 4 SER A 370 ILE A 373 -1 O TYR A 372 N GLN A 351 SHEET 4 G 4 THR A 400 LYS A 402 -1 O ILE A 401 N PHE A 371 LINK OD1 ASN A 173 CA CA A 504 1555 1555 2.65 LINK OE1 GLU A 176 CA CA A 504 1555 1555 2.58 LINK OE2 GLU A 176 CA CA A 504 1555 1555 2.88 LINK OD1 ASN A 382 ZN ZN A 502 1555 1555 2.42 LINK O VAL A 383 ZN ZN A 502 1555 1555 2.52 LINK O PHE A 386 ZN ZN A 502 1555 1555 2.32 LINK OE2 GLU A 396 ZN ZN A 502 1555 1555 2.50 LINK OE1 GLU A 396 ZN ZN A 502 1555 1555 2.58 LINK ZN ZN A 501 O HOH A 797 1555 1555 2.51 LINK ZN ZN A 502 O HOH A 636 1555 1555 2.70 LINK ZN ZN A 502 O HOH A 665 1555 1555 2.67 LINK CA CA A 504 O HOH A 674 1555 1555 2.79 LINK CA CA A 504 O HOH A 773 1555 1555 2.41 LINK CA CA A 504 O HOH A 787 1555 1555 2.35 LINK CA CA A 504 O HOH A 813 1555 1555 2.39 SITE 1 AC1 3 HOH A 796 HOH A 797 HOH A 798 SITE 1 AC2 6 ASN A 382 VAL A 383 PHE A 386 GLU A 396 SITE 2 AC2 6 HOH A 636 HOH A 665 SITE 1 AC3 7 ASN A 173 GLU A 176 GLY A 398 HOH A 674 SITE 2 AC3 7 HOH A 773 HOH A 787 HOH A 813 SITE 1 AC4 12 ASN A 93 ARG A 94 HIS A 126 HIS A 128 SITE 2 AC4 12 MET A 203 ALA A 206 LEU A 207 THR A 208 SITE 3 AC4 12 ALA A 220 GLU A 222 HOH A 623 HOH A 630 CRYST1 53.314 66.928 144.806 90.00 90.00 90.00 P 21 21 21 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 0.018757 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006906 0.00000