HEADER LIGASE 21-FEB-00 1EHI
TITLE D-ALANINE:D-LACTATE LIGASE (LMDDL2) OF VANCOMYCIN-RESISTANT
TITLE 2 LEUCONOSTOC MESENTEROIDES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: D-ALANINE:D-LACTATE LIGASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: LMDDL2;
COMPND 5 EC: 6.3.2.4;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: LEUCONOSTOC MESENTEROIDES;
SOURCE 3 ORGANISM_TAXID: 1245;
SOURCE 4 ATCC: 8293;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5A AND BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PLMDDL2
KEYWDS ATP-BINDING. GRASP MOTIF FOR ATP., LIGASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.P.KUZIN,T.SUN,J.JORCZAK-BAILLASS,V.L.HEALY,C.T.WALSH,
AUTHOR 2 J.R.KNOX
REVDAT 2 24-FEB-09 1EHI 1 VERSN
REVDAT 1 23-MAY-00 1EHI 0
JRNL AUTH A.P.KUZIN,T.SUN,J.JORCZAK-BAILLASS,V.L.HEALY,
JRNL AUTH 2 C.T.WALSH,J.R.KNOX
JRNL TITL ENZYMES OF VANCOMYCIN RESISTANCE: THE STRUCTURE OF
JRNL TITL 2 D-ALANINE-D-LACTATE LIGASE OF NATURALLY RESISTANT
JRNL TITL 3 LEUCONOSTOC MESENTEROIDES.
JRNL REF STRUCTURE FOLD.DES. V. 8 463 2000
JRNL REFN ISSN 0969-2126
JRNL PMID 10801495
JRNL DOI 10.1016/S0969-2126(00)00129-5
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH C.FAN,P.C.MOEWS,C.T.WALSH,J.R.KNOX
REMARK 1 TITL VANCOMYCIN RESISTANCE: STRUCTURE OF
REMARK 1 TITL 2 D-ALANINE:D-ALANINE LIGASE AT 2.3 A RESOLUTION
REMARK 1 REF SCIENCE V. 266 439 1994
REMARK 1 REFN ISSN 0036-8075
REMARK 1 REFERENCE 2
REMARK 1 AUTH C.FAN,I.-S.PARK,C.T.WALSH,J.R.KNOX
REMARK 1 TITL D-ALANINE:D-ALANINE LIGASE: PHOSPHONATE AND
REMARK 1 TITL 2 PHOSPHINATE INTERMEDIATES WITH WILD-TYPE AND THE
REMARK 1 TITL 3 Y216F MUTANT
REMARK 1 REF BIOCHEMISTRY V. 36 2531 1997
REMARK 1 REFN ISSN 0006-2960
REMARK 1 DOI 10.1021/BI962431T
REMARK 2
REMARK 2 RESOLUTION. 2.38 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.851
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.38
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 82.0
REMARK 3 NUMBER OF REFLECTIONS : 27948
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.184
REMARK 3 FREE R VALUE : 0.257
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 951
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5531
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 45
REMARK 3 SOLVENT ATOMS : 213
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.008
REMARK 3 BOND ANGLES (DEGREES) : 1.40
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.20
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT CORRECTION. A 3-
REMARK 3 WAVELENGTH MAD METHOD WAS USED TO DETERMINE STRUCTURE OF THE
REMARK 3 SELENOMET-PROTEIN. A NATIVE DATA SET (A1 AT CHESS) WAS USED TO
REMARK 3 REFINE STRUCTURE.
REMARK 4
REMARK 4 1EHI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-00.
REMARK 100 THE RCSB ID CODE IS RCSB010577.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-AUG-97
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : CHESS
REMARK 200 BEAMLINE : A1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.908
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL (DENZO)
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30564
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.380
REMARK 200 RESOLUTION RANGE LOW (A) : 100.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 82.0
REMARK 200 DATA REDUNDANCY : 3.100
REMARK 200 R MERGE (I) : 0.07200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.38
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.48
REMARK 200 COMPLETENESS FOR SHELL (%) : 47.0
REMARK 200 DATA REDUNDANCY IN SHELL : 2.50
REMARK 200 R MERGE FOR SHELL (I) : 0.21000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: 3-WAVELENGTH MAD NEAR
REMARK 200 SE EDGE (X12C AT BNL)
REMARK 200 SOFTWARE USED: SOLVE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.20
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000 15%, 0.1 M AMMONIUM
REMARK 280 SULFATE, 50MM NACL, 2.4MM DTT, 1MM MGCL2, 3MM ATP, 3MM
REMARK 280 PHOSPHINIC ACID, 50MM MES BUFFER., PH 6.5, VAPOR DIFFUSION,
REMARK 280 SITTING DROP
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 59.10000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.40000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.10000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.40000
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 300 REMARK: THE LIGASE IS A DIMER FORMED OF CHAIN A AND B. HOWEVER,
REMARK 300 PART OF CHAIN B IS MISSING IN THE CRYSTALLOGRAPHIC MODEL.
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 6820 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 27050 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 1
REMARK 465 THR A 2
REMARK 465 TYR A 363
REMARK 465 SER A 364
REMARK 465 PHE A 365
REMARK 465 VAL A 366
REMARK 465 SER A 367
REMARK 465 LEU A 368
REMARK 465 GLY A 369
REMARK 465 GLU A 370
REMARK 465 GLU A 371
REMARK 465 LYS A 372
REMARK 465 ILE A 373
REMARK 465 GLY A 374
REMARK 465 LYS A 375
REMARK 465 PHE A 376
REMARK 465 ASN A 377
REMARK 465 MET B 401
REMARK 465 VAL B 645
REMARK 465 PRO B 646
REMARK 465 ASN B 647
REMARK 465 GLN B 648
REMARK 465 GLY B 649
REMARK 465 SER B 650
REMARK 465 GLY B 651
REMARK 465 ASP B 652
REMARK 465 GLY B 653
REMARK 465 TRP B 654
REMARK 465 TYR B 655
REMARK 465 ASP B 656
REMARK 465 TYR B 657
REMARK 465 ASN B 658
REMARK 465 ASN B 659
REMARK 465 LYS B 660
REMARK 465 PHE B 661
REMARK 465 VAL B 662
REMARK 465 ASP B 663
REMARK 465 ASN B 664
REMARK 465 SER B 665
REMARK 465 ALA B 666
REMARK 465 GLU B 771
REMARK 465 LYS B 772
REMARK 465 ILE B 773
REMARK 465 GLY B 774
REMARK 465 LYS B 775
REMARK 465 PHE B 776
REMARK 465 ASN B 777
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLU B 770 CG CD OE1 OE2
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 61 11.93 -65.16
REMARK 500 LEU A 82 30.33 -99.89
REMARK 500 SER A 90 16.46 -63.80
REMARK 500 ALA A 91 7.76 -153.80
REMARK 500 SER A 186 15.43 57.43
REMARK 500 PHE A 207 7.04 -64.49
REMARK 500 ASN A 232 -98.03 -111.02
REMARK 500 SER A 250 43.95 -86.56
REMARK 500 SER A 265 10.33 -69.59
REMARK 500 PHE A 323 36.85 -144.16
REMARK 500 LEU A 361 30.25 -66.45
REMARK 500 LYS B 403 -64.30 -157.31
REMARK 500 ASN B 413 46.82 -82.68
REMARK 500 GLU B 416 34.92 -98.75
REMARK 500 LEU B 462 21.34 85.05
REMARK 500 VAL B 500 39.45 -145.72
REMARK 500 ASN B 504 22.76 -73.75
REMARK 500 LEU B 505 -37.44 -136.76
REMARK 500 GLN B 584 153.19 179.28
REMARK 500 SER B 586 -29.22 66.13
REMARK 500 SER B 587 -74.35 -158.93
REMARK 500 ALA B 622 67.66 -113.71
REMARK 500 ASN B 632 -105.04 -120.15
REMARK 500 SER B 638 -178.74 -69.24
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 MG A 783 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 316 OE1
REMARK 620 2 GLU A 316 OE2 49.4
REMARK 620 3 ASN A 318 OD1 109.1 76.3
REMARK 620 4 PHY A 782 O5P 145.1 100.6 73.0
REMARK 620 5 ADP A 781 O3B 64.9 92.0 167.4 105.4
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 784 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ADP A 781 O2B
REMARK 620 2 ADP A 781 O2A 76.4
REMARK 620 3 PHY A 782 O4P 69.1 132.0
REMARK 620 4 GLU A 316 OE2 81.0 61.4 80.7
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 MG A 783
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 784
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 781
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PHY A 782
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2DLN RELATED DB: PDB
REMARK 900 D-ALANINE:D-ALANINE LIGASE (DDLB) OF E. COLI COMPLEXED WITH
REMARK 900 PHOSPHINATE AND ADP
REMARK 900 RELATED ID: 1IOV RELATED DB: PDB
REMARK 900 DDLB LIGASE WITH PHOSPHONATE AND ADP
REMARK 900 RELATED ID: 1IOW RELATED DB: PDB
REMARK 900 DDLB Y215F MUTANT WITH PHOSPHINATE AND ADP
DBREF 1EHI A 1 377 UNP P71454 P71454_LEUME 1 377
DBREF 1EHI B 401 777 UNP P71454 P71454_LEUME 1 377
SEQADV 1EHI GLN A 270 UNP P71454 GLU 270 CONFLICT
SEQADV 1EHI GLN B 670 UNP P71454 GLU 270 CONFLICT
SEQRES 1 A 377 MET THR LYS LYS ARG VAL ALA LEU ILE PHE GLY GLY ASN
SEQRES 2 A 377 SER SER GLU HIS ASP VAL SER LYS ARG SER ALA GLN ASN
SEQRES 3 A 377 PHE TYR ASN ALA ILE GLU ALA THR GLY LYS TYR GLU ILE
SEQRES 4 A 377 ILE VAL PHE ALA ILE ALA GLN ASN GLY PHE PHE LEU ASP
SEQRES 5 A 377 THR GLU SER SER LYS LYS ILE LEU ALA LEU GLU ASP GLU
SEQRES 6 A 377 GLN PRO ILE VAL ASP ALA PHE MET LYS THR VAL ASP ALA
SEQRES 7 A 377 SER ASP PRO LEU ALA ARG ILE HIS ALA LEU LYS SER ALA
SEQRES 8 A 377 GLY ASP PHE ASP ILE PHE PHE PRO VAL VAL HIS GLY ASN
SEQRES 9 A 377 LEU GLY GLU ASP GLY THR LEU GLN GLY LEU PHE LYS LEU
SEQRES 10 A 377 LEU ASP LYS PRO TYR VAL GLY ALA PRO LEU ARG GLY HIS
SEQRES 11 A 377 ALA VAL SER PHE ASP LYS ALA LEU THR LYS GLU LEU LEU
SEQRES 12 A 377 THR VAL ASN GLY ILE ARG ASN THR LYS TYR ILE VAL VAL
SEQRES 13 A 377 ASP PRO GLU SER ALA ASN ASN TRP SER TRP ASP LYS ILE
SEQRES 14 A 377 VAL ALA GLU LEU GLY ASN ILE VAL PHE VAL LYS ALA ALA
SEQRES 15 A 377 ASN GLN GLY SER SER VAL GLY ILE SER ARG VAL THR ASN
SEQRES 16 A 377 ALA GLU GLU TYR THR GLU ALA LEU SER ASP SER PHE GLN
SEQRES 17 A 377 TYR ASP TYR LYS VAL LEU ILE GLU GLU ALA VAL ASN GLY
SEQRES 18 A 377 ALA ARG GLU LEU GLU VAL GLY VAL ILE GLY ASN ASP GLN
SEQRES 19 A 377 PRO LEU VAL SER GLU ILE GLY ALA HIS THR VAL PRO ASN
SEQRES 20 A 377 GLN GLY SER GLY ASP GLY TRP TYR ASP TYR ASN ASN LYS
SEQRES 21 A 377 PHE VAL ASP ASN SER ALA VAL HIS PHE GLN ILE PRO ALA
SEQRES 22 A 377 GLN LEU SER PRO GLU VAL THR LYS GLU VAL LYS GLN MET
SEQRES 23 A 377 ALA LEU ASP ALA TYR LYS VAL LEU ASN LEU ARG GLY GLU
SEQRES 24 A 377 ALA ARG MET ASP PHE LEU LEU ASP GLU ASN ASN VAL PRO
SEQRES 25 A 377 TYR LEU GLY GLU PRO ASN THR LEU PRO GLY PHE THR ASN
SEQRES 26 A 377 MET SER LEU PHE LYS ARG LEU TRP ASP TYR SER ASP ILE
SEQRES 27 A 377 ASN ASN ALA LYS LEU VAL ASP MET LEU ILE ASP TYR GLY
SEQRES 28 A 377 PHE GLU ASP PHE ALA GLN ASN LYS LYS LEU SER TYR SER
SEQRES 29 A 377 PHE VAL SER LEU GLY GLU GLU LYS ILE GLY LYS PHE ASN
SEQRES 1 B 377 MET THR LYS LYS ARG VAL ALA LEU ILE PHE GLY GLY ASN
SEQRES 2 B 377 SER SER GLU HIS ASP VAL SER LYS ARG SER ALA GLN ASN
SEQRES 3 B 377 PHE TYR ASN ALA ILE GLU ALA THR GLY LYS TYR GLU ILE
SEQRES 4 B 377 ILE VAL PHE ALA ILE ALA GLN ASN GLY PHE PHE LEU ASP
SEQRES 5 B 377 THR GLU SER SER LYS LYS ILE LEU ALA LEU GLU ASP GLU
SEQRES 6 B 377 GLN PRO ILE VAL ASP ALA PHE MET LYS THR VAL ASP ALA
SEQRES 7 B 377 SER ASP PRO LEU ALA ARG ILE HIS ALA LEU LYS SER ALA
SEQRES 8 B 377 GLY ASP PHE ASP ILE PHE PHE PRO VAL VAL HIS GLY ASN
SEQRES 9 B 377 LEU GLY GLU ASP GLY THR LEU GLN GLY LEU PHE LYS LEU
SEQRES 10 B 377 LEU ASP LYS PRO TYR VAL GLY ALA PRO LEU ARG GLY HIS
SEQRES 11 B 377 ALA VAL SER PHE ASP LYS ALA LEU THR LYS GLU LEU LEU
SEQRES 12 B 377 THR VAL ASN GLY ILE ARG ASN THR LYS TYR ILE VAL VAL
SEQRES 13 B 377 ASP PRO GLU SER ALA ASN ASN TRP SER TRP ASP LYS ILE
SEQRES 14 B 377 VAL ALA GLU LEU GLY ASN ILE VAL PHE VAL LYS ALA ALA
SEQRES 15 B 377 ASN GLN GLY SER SER VAL GLY ILE SER ARG VAL THR ASN
SEQRES 16 B 377 ALA GLU GLU TYR THR GLU ALA LEU SER ASP SER PHE GLN
SEQRES 17 B 377 TYR ASP TYR LYS VAL LEU ILE GLU GLU ALA VAL ASN GLY
SEQRES 18 B 377 ALA ARG GLU LEU GLU VAL GLY VAL ILE GLY ASN ASP GLN
SEQRES 19 B 377 PRO LEU VAL SER GLU ILE GLY ALA HIS THR VAL PRO ASN
SEQRES 20 B 377 GLN GLY SER GLY ASP GLY TRP TYR ASP TYR ASN ASN LYS
SEQRES 21 B 377 PHE VAL ASP ASN SER ALA VAL HIS PHE GLN ILE PRO ALA
SEQRES 22 B 377 GLN LEU SER PRO GLU VAL THR LYS GLU VAL LYS GLN MET
SEQRES 23 B 377 ALA LEU ASP ALA TYR LYS VAL LEU ASN LEU ARG GLY GLU
SEQRES 24 B 377 ALA ARG MET ASP PHE LEU LEU ASP GLU ASN ASN VAL PRO
SEQRES 25 B 377 TYR LEU GLY GLU PRO ASN THR LEU PRO GLY PHE THR ASN
SEQRES 26 B 377 MET SER LEU PHE LYS ARG LEU TRP ASP TYR SER ASP ILE
SEQRES 27 B 377 ASN ASN ALA LYS LEU VAL ASP MET LEU ILE ASP TYR GLY
SEQRES 28 B 377 PHE GLU ASP PHE ALA GLN ASN LYS LYS LEU SER TYR SER
SEQRES 29 B 377 PHE VAL SER LEU GLY GLU GLU LYS ILE GLY LYS PHE ASN
HET MG A 783 1
HET MG A 784 1
HET ADP A 781 27
HET PHY A 782 16
HETNAM MG MAGNESIUM ION
HETNAM ADP ADENOSINE-5'-DIPHOSPHATE
HETNAM PHY 1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-
HETNAM 2 PHY PHOSPHINIC ACID
FORMUL 3 MG 2(MG 2+)
FORMUL 5 ADP C10 H15 N5 O10 P2
FORMUL 6 PHY C6 H15 N O7 P2
FORMUL 7 HOH *213(H2 O)
HELIX 1 1 GLU A 16 GLY A 35 1 20
HELIX 2 2 ASP A 52 ALA A 61 1 10
HELIX 3 3 ASP A 64 LYS A 74 1 11
HELIX 4 4 ILE A 85 SER A 90 5 6
HELIX 5 5 GLY A 109 LEU A 118 1 10
HELIX 6 6 PRO A 126 ASP A 135 1 10
HELIX 7 7 ASP A 135 VAL A 145 1 11
HELIX 8 8 GLU A 159 TRP A 164 5 6
HELIX 9 9 SER A 165 GLY A 174 1 10
HELIX 10 10 ASN A 195 PHE A 207 1 13
HELIX 11 11 ASP A 256 PHE A 261 1 6
HELIX 12 12 SER A 276 LEU A 294 1 19
HELIX 13 13 SER A 327 ARG A 331 5 5
HELIX 14 14 ARG A 331 ASP A 337 5 7
HELIX 15 15 ASN A 339 LEU A 361 1 23
HELIX 16 16 GLU B 416 ALA B 433 1 18
HELIX 17 17 ASP B 452 ALA B 461 1 10
HELIX 18 18 ASP B 464 LYS B 474 1 11
HELIX 19 19 LEU B 482 ALA B 487 1 6
HELIX 20 20 GLY B 509 LEU B 518 1 10
HELIX 21 21 PRO B 526 ASP B 535 1 10
HELIX 22 22 ASP B 535 ASN B 546 1 12
HELIX 23 23 GLU B 559 TRP B 564 5 6
HELIX 24 24 SER B 565 LEU B 573 1 9
HELIX 25 25 ASN B 595 PHE B 607 1 13
HELIX 26 26 SER B 676 LEU B 694 1 19
HELIX 27 27 SER B 727 ARG B 731 5 5
HELIX 28 28 LEU B 732 ASP B 737 5 6
HELIX 29 29 ASN B 739 LYS B 759 1 21
SHEET 1 A 3 TYR A 37 ILE A 44 0
SHEET 2 A 3 LYS A 4 GLY A 11 1 O LYS A 4 N GLU A 38
SHEET 3 A 3 ILE A 96 VAL A 100 1 O ILE A 96 N ALA A 7
SHEET 1 B 4 TYR A 153 VAL A 156 0
SHEET 2 B 4 VAL A 213 GLU A 217 -1 N VAL A 213 O VAL A 156
SHEET 3 B 4 VAL A 177 ALA A 181 -1 N PHE A 178 O GLU A 216
SHEET 4 B 4 ILE A 190 VAL A 193 -1 N SER A 191 O VAL A 179
SHEET 1 C 5 HIS A 268 GLN A 270 0
SHEET 2 C 5 LEU A 236 THR A 244 -1 N ALA A 242 O GLN A 270
SHEET 3 C 5 GLU A 224 GLY A 231 -1 N GLU A 224 O HIS A 243
SHEET 4 C 5 GLY A 298 LEU A 306 -1 O GLY A 298 N GLY A 231
SHEET 5 C 5 PRO A 312 ASN A 318 -1 N TYR A 313 O LEU A 305
SHEET 1 D 4 PHE B 450 LEU B 451 0
SHEET 2 D 4 TYR B 437 ILE B 444 -1 O ALA B 443 N LEU B 451
SHEET 3 D 4 LYS B 404 GLY B 411 1 O LYS B 404 N GLU B 438
SHEET 4 D 4 ILE B 496 PRO B 499 1 O ILE B 496 N ALA B 407
SHEET 1 E 4 TYR B 553 VAL B 556 0
SHEET 2 E 4 VAL B 613 GLU B 617 -1 O VAL B 613 N VAL B 556
SHEET 3 E 4 VAL B 577 ALA B 581 -1 N PHE B 578 O GLU B 616
SHEET 4 E 4 SER B 591 VAL B 593 -1 N SER B 591 O VAL B 579
SHEET 1 F 5 PHE B 669 GLN B 670 0
SHEET 2 F 5 LEU B 636 HIS B 643 -1 O ALA B 642 N GLN B 670
SHEET 3 F 5 ARG B 623 GLY B 631 -1 O GLU B 624 N HIS B 643
SHEET 4 F 5 GLY B 698 LEU B 706 -1 N GLY B 698 O GLY B 631
SHEET 5 F 5 PRO B 712 ASN B 718 -1 N TYR B 713 O LEU B 705
LINK MG MG A 783 OE1 GLU A 316 1555 1555 2.31
LINK MG MG A 783 OE2 GLU A 316 1555 1555 2.83
LINK MG MG A 783 OD1 ASN A 318 1555 1555 2.54
LINK MG MG A 783 O5P PHY A 782 1555 1555 2.20
LINK MG MG A 783 O3B ADP A 781 1555 1555 2.48
LINK MG MG A 784 O2B ADP A 781 1555 1555 2.51
LINK MG MG A 784 O2A ADP A 781 1555 1555 2.66
LINK MG MG A 784 O4P PHY A 782 1555 1555 2.25
LINK MG MG A 784 OE2 GLU A 316 1555 1555 2.65
CISPEP 1 ILE A 271 PRO A 272 0 -0.09
CISPEP 2 ILE B 671 PRO B 672 0 -0.01
SITE 1 AC1 4 GLU A 316 ASN A 318 ADP A 781 PHY A 782
SITE 1 AC2 4 ASP A 303 GLU A 316 ADP A 781 PHY A 782
SITE 1 AC3 22 THR A 151 PHE A 178 LYS A 180 GLN A 184
SITE 2 AC3 22 GLY A 185 SER A 186 SER A 187 ILE A 190
SITE 3 AC3 22 GLU A 216 GLU A 217 ALA A 218 VAL A 219
SITE 4 AC3 22 GLU A 224 TRP A 254 TYR A 255 LYS A 260
SITE 5 AC3 22 LEU A 305 GLU A 316 PHY A 782 MG A 783
SITE 6 AC3 22 MG A 784 HOH A 847
SITE 1 AC4 17 GLU A 16 SER A 186 LYS A 260 PHE A 261
SITE 2 AC4 17 ARG A 301 ASP A 303 GLU A 316 ASN A 318
SITE 3 AC4 17 GLY A 322 MET A 326 SER A 327 ADP A 781
SITE 4 AC4 17 MG A 783 MG A 784 HOH A 824 HOH A 834
SITE 5 AC4 17 HOH A 924
CRYST1 118.200 90.800 82.100 90.00 92.10 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 0.008460 0.000000 0.000310 0.00000
SCALE2 0.000000 0.011013 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012188 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
