HEADER TRANSPORT PROTEIN 08-SEP-05 2AYS TITLE A CONSERVED NON-METALLIC BINDING SITE IN THE C-TERMINAL LOBE OF TITLE 2 LACTOFERRIN: STRUCTURE OF THE COMPLEX OF C-TERMINAL LOBE OF BOVINE TITLE 3 LACTOFERRIN WITH N-ACETYL GALACTOSAMINE AT 1.86 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACTOTRANSFERRIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LACTOFERRIN LOBE; COMPND 5 SYNONYM: LACTOFERRIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS C-LOBE, COMPLEX, LACTOFERRIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.SINGH,T.JABEEN,S.SHARMA,T.P.SINGH REVDAT 6 20-NOV-24 2AYS 1 REMARK REVDAT 5 25-OCT-23 2AYS 1 HETSYN REVDAT 4 29-JUL-20 2AYS 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 13-JUL-11 2AYS 1 VERSN REVDAT 2 24-FEB-09 2AYS 1 VERSN REVDAT 1 20-SEP-05 2AYS 0 JRNL AUTH N.SINGH,T.JABEEN,S.SHARMA,T.P.SINGH JRNL TITL A CONSERVED NON-METALLIC BINDING SITE IN THE C-TERMINAL LOBE JRNL TITL 2 OF LACTOFERRIN: STRUCTURE OF THE COMPLEX OF C-TERMINAL LOBE JRNL TITL 3 OF BOVINE LACTOFERRIN WITH N-ACETYL GALACTOSAMINE AT 1.86 A JRNL TITL 4 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 31367 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.100 REMARK 3 FREE R VALUE TEST SET COUNT : 661 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1746 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2593 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 152 REMARK 3 SOLVENT ATOMS : 250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.67000 REMARK 3 B22 (A**2) : -0.41000 REMARK 3 B33 (A**2) : -0.68000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.69000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.135 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.923 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2808 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3823 ; 1.781 ; 2.016 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 338 ; 4.620 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 465 ;18.886 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 452 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2027 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1233 ; 0.265 ; 0.300 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): 317 ; 0.177 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 4 ; 0.186 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 35 ; 0.297 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.140 ; 0.500 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): 1688 ; 1.126 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2692 ; 2.161 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1120 ; 3.065 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1131 ; 5.176 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AYS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034463. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-05 REMARK 200 TEMPERATURE (KELVIN) : 283 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : Y REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31367 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 63.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.6 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1NKX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, 25% POLYETHYLENE GLYCOL REMARK 280 MONOMETHYL ETHER 550, 0.01M ZINC SULPHATE , PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 25.20050 REMARK 290 SMTRY3 2 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 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 THR A 677 REMARK 465 SER A 678 REMARK 465 PRO A 679 REMARK 465 LEU A 680 REMARK 465 PHE A 686 REMARK 465 LEU A 687 REMARK 465 THR A 688 REMARK 465 ARG A 689 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 471 SD MET A 471 CE -0.386 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 378 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 453 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 536 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES 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 PRO A 429 157.70 -48.27 REMARK 500 ASP A 462 -0.91 76.07 REMARK 500 TRP A 467 -61.42 -145.69 REMARK 500 ALA A 482 45.32 -83.42 REMARK 500 ASP A 509 -71.94 -3.51 REMARK 500 VAL A 543 -156.04 -139.46 REMARK 500 THR A 557 -8.20 58.28 REMARK 500 SER A 634 39.57 -171.34 REMARK 500 LEU A 640 -46.41 73.46 REMARK 500 ARG A 654 63.14 30.15 REMARK 500 ALA A 683 24.22 -171.54 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 FE A1686 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 395 OD1 REMARK 620 2 TYR A 433 OH 86.0 REMARK 620 3 TYR A 526 OH 172.1 99.8 REMARK 620 4 HIS A 595 NE2 87.7 96.5 86.4 REMARK 620 5 CO3 A1687 O1 89.3 158.8 87.1 104.1 REMARK 620 6 CO3 A1687 O2 89.3 94.2 95.5 168.7 65.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 588 NE2 REMARK 620 2 HOH A2173 O 103.1 REMARK 620 3 HOH A2174 O 126.5 74.0 REMARK 620 4 HOH A2212 O 106.9 68.5 119.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 659 OE1 REMARK 620 2 GLU A 659 OE2 59.5 REMARK 620 3 HOH A2213 O 102.3 97.3 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NKX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A PROTEOLYTICALLY GENERATED FUNCTIONAL REMARK 900 MONOFERRIC C-LOBE OF BOVINE LACTOFERRIN AT 1.9A RESOLUTION REMARK 900 RELATED ID: 1SDX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A PROTEOLYTICALLY GENERATED CRYSTAL STRUCTURE REMARK 900 OF THE ZINC SATURATED C-TERMINAL HALF OF BOVINE LACTOFERRIN AT 2.0 REMARK 900 A RESOLUTION REVEALS TWO ADDITIONAL ZINC BINDING SITES DBREF 2AYS A 342 689 UNP P24627 TRFL_BOVIN 361 708 SEQADV 2AYS LYS A 565 UNP P24627 ASN 584 SEE REMARK 999 SEQADV 2AYS GLU A 608 UNP P24627 LYS 627 SEE REMARK 999 SEQRES 1 A 348 TYR THR ARG VAL VAL TRP CYS ALA VAL GLY PRO GLU GLU SEQRES 2 A 348 GLN LYS LYS CYS GLN GLN TRP SER GLN GLN SER GLY GLN SEQRES 3 A 348 ASN VAL THR CYS ALA THR ALA SER THR THR ASP ASP CYS SEQRES 4 A 348 ILE VAL LEU VAL LEU LYS GLY GLU ALA ASP ALA LEU ASN SEQRES 5 A 348 LEU ASP GLY GLY TYR ILE TYR THR ALA GLY LYS CYS GLY SEQRES 6 A 348 LEU VAL PRO VAL LEU ALA GLU ASN ARG LYS SER SER LYS SEQRES 7 A 348 HIS SER SER LEU ASP CYS VAL LEU ARG PRO THR GLU GLY SEQRES 8 A 348 TYR LEU ALA VAL ALA VAL VAL LYS LYS ALA ASN GLU GLY SEQRES 9 A 348 LEU THR TRP ASN SER LEU LYS ASP LYS LYS SER CYS HIS SEQRES 10 A 348 THR ALA VAL ASP ARG THR ALA GLY TRP ASN ILE PRO MET SEQRES 11 A 348 GLY LEU ILE VAL ASN GLN THR GLY SER CYS ALA PHE ASP SEQRES 12 A 348 GLU PHE PHE SER GLN SER CYS ALA PRO GLY ALA ASP PRO SEQRES 13 A 348 LYS SER ARG LEU CYS ALA LEU CYS ALA GLY ASP ASP GLN SEQRES 14 A 348 GLY LEU ASP LYS CYS VAL PRO ASN SER LYS GLU LYS TYR SEQRES 15 A 348 TYR GLY TYR THR GLY ALA PHE ARG CYS LEU ALA GLU ASP SEQRES 16 A 348 VAL GLY ASP VAL ALA PHE VAL LYS ASN ASP THR VAL TRP SEQRES 17 A 348 GLU ASN THR ASN GLY GLU SER THR ALA ASP TRP ALA LYS SEQRES 18 A 348 ASN LEU LYS ARG GLU ASP PHE ARG LEU LEU CYS LEU ASP SEQRES 19 A 348 GLY THR ARG LYS PRO VAL THR GLU ALA GLN SER CYS HIS SEQRES 20 A 348 LEU ALA VAL ALA PRO ASN HIS ALA VAL VAL SER ARG SER SEQRES 21 A 348 ASP ARG ALA ALA HIS VAL GLU GLN VAL LEU LEU HIS GLN SEQRES 22 A 348 GLN ALA LEU PHE GLY LYS ASN GLY LYS ASN CYS PRO ASP SEQRES 23 A 348 LYS PHE CYS LEU PHE LYS SER GLU THR LYS ASN LEU LEU SEQRES 24 A 348 PHE ASN ASP ASN THR GLU CYS LEU ALA LYS LEU GLY GLY SEQRES 25 A 348 ARG PRO THR TYR GLU GLU TYR LEU GLY THR GLU TYR VAL SEQRES 26 A 348 THR ALA ILE ALA ASN LEU LYS LYS CYS SER THR SER PRO SEQRES 27 A 348 LEU LEU GLU ALA CYS ALA PHE LEU THR ARG MODRES 2AYS ASN A 368 ASN GLYCOSYLATION SITE MODRES 2AYS ASN A 476 ASN GLYCOSYLATION SITE MODRES 2AYS ASN A 545 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN C 4 11 HET MAN C 5 11 HET MAN C 6 11 HET NAG A 1 14 HET A2G A 690 15 HET ZN A1001 1 HET ZN A1002 1 HET FE A1686 1 HET CO3 A1687 4 HET SO4 A2001 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETNAM ZN ZINC ION HETNAM FE FE (III) ION HETNAM CO3 CARBONATE ION HETNAM SO4 SULFATE ION 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 BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN A2G N-ACETYL-ALPHA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 A2G ALPHA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 A2G ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-2-DEOXY-2-AMINO- HETSYN 4 A2G GALACTOSE FORMUL 2 NAG 5(C8 H15 N O6) FORMUL 2 BMA 2(C6 H12 O6) FORMUL 3 MAN 3(C6 H12 O6) FORMUL 5 A2G C8 H15 N O6 FORMUL 6 ZN 2(ZN 2+) FORMUL 8 FE FE 3+ FORMUL 9 CO3 C O3 2- FORMUL 10 SO4 O4 S 2- FORMUL 11 HOH *250(H2 O) HELIX 1 1 GLY A 351 SER A 365 1 15 HELIX 2 2 THR A 376 LYS A 386 1 11 HELIX 3 3 ASP A 395 CYS A 405 1 11 HELIX 4 4 ASP A 424 ARG A 428 5 5 HELIX 5 5 THR A 447 LEU A 451 5 5 HELIX 6 6 TRP A 467 GLY A 479 1 13 HELIX 7 7 SER A 499 ALA A 503 5 5 HELIX 8 8 TYR A 524 GLU A 535 1 12 HELIX 9 9 ASN A 545 ASN A 551 1 7 HELIX 10 10 LYS A 565 GLU A 567 5 3 HELIX 11 11 PRO A 580 CYS A 587 5 8 HELIX 12 12 ARG A 603 GLY A 619 1 17 HELIX 13 13 THR A 656 GLY A 662 1 7 HELIX 14 14 GLY A 662 LYS A 674 1 13 SHEET 1 A 2 VAL A 345 VAL A 350 0 SHEET 2 A 2 VAL A 369 ALA A 374 1 O THR A 370 N TRP A 347 SHEET 1 B 4 ALA A 391 LEU A 394 0 SHEET 2 B 4 ALA A 596 ARG A 600 -1 O ALA A 596 N LEU A 394 SHEET 3 B 4 LEU A 407 ARG A 415 -1 N VAL A 410 O VAL A 597 SHEET 4 B 4 THR A 645 ALA A 649 -1 O ALA A 649 N ALA A 412 SHEET 1 C 6 GLN A 489 CYS A 491 0 SHEET 2 C 6 LYS A 455 HIS A 458 1 N HIS A 458 O CYS A 491 SHEET 3 C 6 VAL A 540 LYS A 544 1 O PHE A 542 N CYS A 457 SHEET 4 C 6 TYR A 433 LYS A 440 -1 N VAL A 438 O ALA A 541 SHEET 5 C 6 PHE A 569 LEU A 572 -1 O ARG A 570 N VAL A 439 SHEET 6 C 6 ARG A 578 LYS A 579 -1 O LYS A 579 N LEU A 571 SHEET 1 D 5 GLN A 489 CYS A 491 0 SHEET 2 D 5 LYS A 455 HIS A 458 1 N HIS A 458 O CYS A 491 SHEET 3 D 5 VAL A 540 LYS A 544 1 O PHE A 542 N CYS A 457 SHEET 4 D 5 TYR A 433 LYS A 440 -1 N VAL A 438 O ALA A 541 SHEET 5 D 5 ALA A 590 ALA A 592 -1 O ALA A 592 N TYR A 433 SSBOND 1 CYS A 348 CYS A 380 1555 1555 2.01 SSBOND 2 CYS A 358 CYS A 371 1555 1555 2.02 SSBOND 3 CYS A 405 CYS A 684 1555 1555 2.04 SSBOND 4 CYS A 425 CYS A 647 1555 1555 2.01 SSBOND 5 CYS A 457 CYS A 532 1555 1555 2.01 SSBOND 6 CYS A 481 CYS A 675 1555 1555 2.01 SSBOND 7 CYS A 491 CYS A 505 1555 1555 2.02 SSBOND 8 CYS A 502 CYS A 515 1555 1555 2.02 SSBOND 9 CYS A 573 CYS A 587 1555 1555 2.03 SSBOND 10 CYS A 625 CYS A 630 1555 1555 2.07 LINK C1 NAG A 1 ND2 ASN A 368 1555 1555 1.45 LINK ND2 ASN A 476 C1 NAG B 1 1555 1555 1.43 LINK ND2 ASN A 545 C1 NAG C 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.43 LINK O4 BMA C 3 C1 MAN C 4 1555 1555 1.44 LINK O4 MAN C 4 C1 MAN C 5 1555 1555 1.45 LINK O4 MAN C 5 C1 MAN C 6 1555 1555 1.46 LINK OD1 ASP A 395 FE FE A1686 1555 1555 2.07 LINK OH TYR A 433 FE FE A1686 1555 1555 1.95 LINK OH TYR A 526 FE FE A1686 1555 1555 1.88 LINK NE2 HIS A 588 ZN ZN A1002 1555 1555 2.03 LINK NE2 HIS A 595 FE FE A1686 1555 1555 2.18 LINK OE1 GLU A 659 ZN ZN A1001 1555 1555 2.32 LINK OE2 GLU A 659 ZN ZN A1001 1555 1555 2.13 LINK ZN ZN A1001 O HOH A2213 1555 1555 2.13 LINK ZN ZN A1002 O HOH A2173 1555 1555 2.29 LINK ZN ZN A1002 O HOH A2174 1555 1555 2.03 LINK ZN ZN A1002 O HOH A2212 1555 1555 2.01 LINK FE FE A1686 O1 CO3 A1687 1555 1555 2.10 LINK FE FE A1686 O2 CO3 A1687 1555 1555 2.09 CRYST1 63.494 50.401 65.914 90.00 107.83 90.00 P 1 21 1 2 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 0.015750 0.000000 0.005067 0.00000 SCALE2 0.000000 0.019841 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015937 0.00000